Corynebacterium glutamicum genes encoding stress, resistance and tolerance proteins

ABSTRACT

Isolated nucleic acid molecules, designated SRT nucleic acid molecules, which encode novel SRT proteins from  Corynebacterium glutamicum  are described. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing SRT nucleic acid molecules, and host cells into which the expression vectors have been introduced. The invention still further provides isolated SRT proteins, mutated SRT proteins, fusion proteins, antigenic peptides and methods for the improvement of production of a desired compound from  C. glutamicum  based on genetic engineering of SRT genes in this organism.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.09/603,208 which claims priority to prior filed U.S. Provisional PatentApplication Ser. No. 60/141,031, filed Jun. 25, 1999, U.S. ProvisionalPatent Application Ser. No. 60/142,692, filed Jul. 1, 1999, and also toU.S. Provisional Patent Application Ser. No. 60/151,214, filed Aug. 27,1999. This application also claims priority to German Patent ApplicationNo. 19930429.7, filed Jul. 1, 1999, German Patent Application No.19931413.6, filed Jul. 8, 1999, German Patent Application No.19931457.8, filed Jul. 8, 1999, German Patent Application No.19931541.8, filed Jul. 8, 1999, German Patent Application No.19932209.0, filed Jul. 9, 1999, German Patent Application No.19932230.9, filed Jul. 9, 1999, German Patent Application No.19932914.1, filed Jul. 14, 1999, German Patent Application No.19940764.9, filed Aug. 27, 1999, and German Patent Application No.19941382.7, filed Aug. 31, 1999. The entire contents of all of theaforementioned applications are hereby expressly incorporated herein intheir entirety by this reference.

BACKGROUND OF THE INVENTION

Certain products and by-products of naturally-occurring metabolicprocesses in cells have utility in a wide array of industries, includingthe food, feed, cosmetics, and pharmaceutical industries. Thesemolecules, collectively termed ‘fine chemicals’, include organic acids,both proteinogenic and non-proteinogenic amino acids, nucleotides andnucleosides, lipids and fatty acids, diols, carbohydrates, aromaticcompounds, vitamins and cofactors, and enzymes. Their production is mostconveniently performed through large-scale culture of bacteria developedto produce and secrete large quantities of a particular desiredmolecule. One particularly useful organism for this purpose isCorynebacterium glutamicum, a gram positive, nonpathogenic bacterium.Through strain selection, a number of mutant strains have been developedwhich produce an array of desirable compounds. However, selection ofstrains improved for the production of a particular molecule is atime-consuming and difficult process.

SUMMARY OF THE INVENTION

The invention provides novel bacterial nucleic acid molecules which havea variety of uses. These uses include the identification ofmicroorganisms which can be used to produce fine chemicals, themodulation of fine chemical production in C. glutamicum or relatedbacteria, the typing or identification of C. glutamicum or relatedbacteria, as reference points for mapping the C. glutamicum genome, andas markers for transformation. These novel nucleic acid molecules encodeproteins, referred to herein as stress, resistance and tolerance (SRT)proteins.

C. glutamicum is a gram positive, aerobic bacterium which is commonlyused in industry for the large-scale production of a variety of finechemicals, and also for the degradation of hydrocarbons (such as inpetroleum spills) and for the oxidation of terpenoids. The SRT nucleicacid molecules of the invention, therefore, can be used to identifymicroorganisms which can be used to produce fine chemicals, e.g., byfermentation processes. Modulation of the expression of the SRT nucleicacids of the invention, or modification of the sequence of the SRTnucleic acid molecules of the invention, can be used to modulate theproduction of one or more fine chemicals from a microorganism (e.g., toimprove the yield or production of one or more fine chemicals from aCorynebacterium or Brevibacterium species).

The SRT nucleic acids of the invention may also be used to identify anorganism as being Corynebacterium glutamicum or a close relativethereof, or to identify the presence of C. glutamicum or a relativethereof in a mixed population of microorganisms. The invention providesthe nucleic acid sequences of a number of C. glutamicum genes; byprobing the extracted genomic DNA of a culture of a unique or mixedpopulation of microorganisms under stringent conditions with a probespanning a region of a C. glutamicum gene which is unique to thisorganism, one can ascertain whether this organism is present. AlthoughCorynebacterium glutamicum itself is nonpathogenic, it is related tospecies pathogenic in humans, such as Corynebacterium diphtheriae (thecausative agent of diphtheria); the detection of such organisms is ofsignificant clinical relevance.

The SRT nucleic acid molecules of the invention may also serve asreference points for mapping of the C. glutamicum genome, or of genomesof related organisms. Similarly, these molecules, or variants orportions thereof, may serve as markers for genetically engineeredCorynebacterium or Brevibacterium species.

The SRT proteins encoded by the novel nucleic acid molecules of theinvention are capable of, for example, permitting C. glutamicum tosurvive in a setting which is either chemically or environmentallyhazardous to this microorganism. Given the availability of cloningvectors for use in Corynebacterium glutamicum, such as those disclosedin Sinskey et al., U.S. Pat. No. 4,649,119, and techniques for geneticmanipulation of C. glutamicum and the related Brevibacterium species(e.g., lactofermentum) (Yoshihama et al, J. Bacteriol. 162: 591-597(1985); Katsumata et al., J. Bacteriol. 159: 306-311 (1984); andSantamaria et al., J. Gen. Microbiol. 130: 2237-2246 (1984)), thenucleic acid molecules of the invention may be utilized in the geneticengineering of this organism to make it a better or more efficientproducer of one or more fine chemicals, through the ability of theseproteins to permit growth and multiplication of C. glutamicum (and alsocontinuous production of one or more fine chemicals) under circumstanceswhich would normally impede growth of the organism, such as thoseconditions frequently encountered during large-scale fermentativegrowth. For example, by overexpressing or engineering a heat-shockinduced protease molecule such that it is optimized in activity, one mayincrease the ability of the bacterium to degrade incorrectly foldedproteins when the bacterium is challenged with high temperatures. Byhaving fewer misfolded (and possibly misregulated or nonfunctional)proteins to interfere with normal reaction mechanisms in the cell, thecell is increased in its ability to function normally in such a culture,which should in turn provide increased viability. This overall increasein number of cells having greater viability and activity in the cultureshould also result in an increase in yield, production, and/orefficiency of production of one or more desired fine chemicals, due atleast to the relatively greater number of cells producing thesechemicals in the culture.

This invention provides novel SRT nucleic acid molecules which encodeSRT proteins which are capable of, for example, permitting C. glutamicumto survive in a setting which is either chemically or environmentallyhazardous to this microorganism. Nucleic acid molecules encoding an SRTprotein are referred to herein as SRT nucleic acid molecules. In apreferred embodiment, the SRT protein participates in metabolic pathwayspermitting C. glutamicum to survive in a setting which is eitherchemically or environmentally hazardous to this microorganism. Examplesof such proteins include those encoded by the genes set forth in Table1.

Accordingly, one aspect of the invention pertains to isolated nucleicacid molecules (e.g., cDNAs, DNAs, or RNAs) comprising a nucleotidesequence encoding an SRT protein or biologically active portionsthereof, as well as nucleic acid fragments suitable as primers orhybridization probes for the detection or amplification of SRT-encodingnucleic acid (e.g., DNA or mRNA). In particularly preferred embodiments,the isolated nucleic acid molecule comprises one of the nucleotidesequences set forth in Appendix A or the coding region or a complementthereof of one of these nucleotide sequences. In other particularlypreferred embodiments, the isolated nucleic acid molecule of theinvention comprises a nucleotide sequence which hybridizes to or is atleast about 50%, preferably at least about 60%, more preferably at leastabout 70%, 80% or 90%, and even more preferably at least about 95%, 96%,97%, 98%, 99% or more homologous to a nucleotide sequence set forth inAppendix A, or a portion thereof. In other preferred embodiments, theisolated nucleic acid molecule encodes one of the amino acid sequencesset forth in Appendix B. The preferred SRT proteins of the presentinvention also preferably possess at least one of the SRT activitiesdescribed herein.

In another embodiment, the isolated nucleic acid molecule encodes aprotein or portion thereof wherein the protein or portion thereofincludes an amino acid sequence which is sufficiently homologous to anamino acid sequence of Appendix B, e.g., sufficiently homologous to anamino acid sequence of Appendix B such that the protein or portionthereof maintains an SRT activity. Preferably, the protein or portionthereof encoded by the nucleic acid molecule maintains the ability toincrease the survival of C. glutamicum in a setting which is eitherchemically or environmentally hazardous to this microorganism. In oneembodiment, the protein encoded by the nucleic acid molecule is at leastabout 50%, preferably at least about 60%, and more preferably at leastabout 70%, 80%, or 90% and most preferably at least about 95%, 96%, 97%,98%, or 99% or more homologous to an amino acid sequence of Appendix B(e.g., an entire amino acid sequence selected from those sequences setforth in Appendix B). In another preferred embodiment, the protein is afull length C. glutamicum protein which is substantially homologous toan entire amino acid sequence of Appendix B (encoded by an open readingframe shown in Appendix A).

In another preferred embodiment, the isolated nucleic acid molecule isderived from C. glutamicum and encodes a protein (e.g., an SRT fusionprotein) which includes a biologically active domain which is at leastabout 50% or more homologous to one of the amino acid sequences ofAppendix B and has the ability to increase the survival of C. glutamicumin a setting which is either chemically or environmentally hazardous tothis microorganism, or possesses one or more of the activities set forthin Table 1, and which also includes heterologous nucleic acid sequencesencoding a heterologous polypeptide or regulatory regions.

In another embodiment, the isolated nucleic acid molecule is at least 15nucleotides in length and hybridizes under stringent conditions to anucleic acid molecule comprising a nucleotide sequence of Appendix A.Preferably, the isolated nucleic acid molecule corresponds to anaturally-occurring nucleic acid molecule. More preferably, the isolatednucleic acid encodes a naturally-occurring C. glutamicum SRT protein, ora biologically active portion thereof.

Another aspect of the invention pertains to vectors, e.g., recombinantexpression vectors, containing the nucleic acid molecules of theinvention, and host cells into which such vectors have been introduced.In one embodiment, such a host cell is used to produce an SRT protein byculturing the host cell in a suitable medium. The SRT protein can bethen isolated from the medium or the host cell.

Yet another aspect of the invention pertains to a genetically alteredmicroorganism in which an SRT gene has been introduced or altered. Inone embodiment, the genome of the microorganism has been altered by theintroduction of a nucleic acid molecule of the invention encodingwild-type or mutated SRT sequence as a transgene. In another embodiment,an endogenous SRT gene within the genome of the microorganism has beenaltered, e.g., functionally disrupted, by homologous recombination withan altered SRT gene. In another embodiment, an endogenous or introducedSRT gene in a microorganism has been altered by one or more pointmutations, deletions, or inversions, but still encodes a functional SRTprotein. In still another embodiment, one or more of the regulatoryregions (e.g., a promoter, repressor, or inducer) of a SRT gene in amicroorganism has been altered (e.g., by deletion, truncation,inversion, or point mutation) such that the expression of the SRT geneis modulated. In a preferred embodiment, the microorganism belongs tothe genus Corynebacterium or Brevibacterium, with Corynebacteriumglutamicum being particularly preferred. In a preferred embodiment, themicroorganism is also utilized for the production of a desired compound,such as an amino acid, with lysine being particularly preferred.

In another aspect, the invention provides a method of identifying thepresence or activity of Cornyebacterium diphtheriae in a subject. Thismethod includes detection of one or more of the nucleic acid or aminoacid sequences of the invention (e.g., the sequences set forth inAppendix A or Appendix B) in a subject, thereby detecting the presenceor activity of Corynebacterium diphtheriae in the subject.

Still another aspect of the invention pertains to an isolated SRTprotein or a portion, e.g., a biologically active portion, thereof. In apreferred embodiment, the isolated SRT protein or portion thereofpossesses the ability to increase the survival of C. glutamicum in asetting which is either chemically or environmentally hazardous to thismicroorganism. In another preferred embodiment, the isolated SRT proteinor portion thereof is sufficiently homologous to an amino acid sequenceof Appendix B such that the protein or portion thereof maintains theability to increase the survival of C. glutamicum in a setting which iseither chemically or environmentally hazardous to this microorganism.

The invention also provides an isolated preparation of an SRT protein.In preferred embodiments, the SRT protein comprises an amino acidsequence of Appendix B. In another preferred embodiment, the inventionpertains to an isolated full length protein which is substantiallyhomologous to an entire amino acid sequence of Appendix B (encoded by anopen reading frame set forth in Appendix A). In yet another embodiment,the protein is at least about 50%, preferably at least about 60%, andmore preferably at least about 70%, 80%, or 90%, and most preferably atleast about 95%, 96%, 97%, 98%, or 99% or more homologous to an entireamino acid sequence of Appendix B. In other embodiments, the isolatedSRT protein comprises an amino acid sequence which is at least about 50%or more homologous to one of the amino acid sequences of Appendix B andis able to improve the survival rate of C. glutamicum in a setting whichis either chemically or environmentally hazardous to this microorganism,or has one or more of the activities set forth in Table 1.

Alternatively, the isolated SRT protein can comprise an amino acidsequence which is encoded by a nucleotide sequence which hybridizes,e.g., hybridizes under stringent conditions, or is at least about 50%,preferably at least about 60%, more preferably at least about 70%, 80%,or 90%, and even more preferably at least about 95%, 96%, 97%, 98,%, or99% or more homologous, to a nucleotide sequence of Appendix B. It isalso preferred that the preferred forms of SRT proteins also have one ormore of the SRT bioactivities described herein.

The SRT polypeptide, or a biologically active portion thereof, can beoperatively linked to a non-SRT polypeptide to form a fusion protein. Inpreferred embodiments, this fusion protein has an activity which differsfrom that of the SRT protein alone. In other preferred embodiments, thisfusion protein results in increased yields, production, and/orefficiency of production of a desired fine chemical from C. glutamicum.In particularly preferred embodiments, integration of this fusionprotein into a host cell modulates the production of a desired compoundfrom the cell.

In another aspect, the invention provides methods for screeningmolecules which modulate the activity of an SRT protein, either byinteracting with the protein itself or a substrate or binding partner ofthe SRT protein, or by modulating the transcription or translation of anSRT nucleic acid molecule of the invention.

Another aspect of the invention pertains to a method for producing afine chemical. This method involves the culturing of a cell containing avector directing the expression of an SRT nucleic acid molecule of theinvention, such that a fine chemical is produced. In a preferredembodiment, this method further includes the step of obtaining a cellcontaining such a vector, in which a cell is transfected with a vectordirecting the expression of an SRT nucleic acid. In another preferredembodiment, this method further includes the step of recovering the finechemical from the culture. In a particularly preferred embodiment, thecell is from the genus Corynebacterium or Brevibacterium, or is selectedfrom those strains set forth in Table 3.

Another aspect of the invention pertains to methods for modulatingproduction of a molecule from a microorganism. Such methods includecontacting the cell with an agent which modulates SRT protein activityor SRT nucleic acid expression such that a cell associated activity isaltered relative to this same activity in the absence of the agent. In apreferred embodiment, the cell is modulated in resistance to one or moretoxic chemicals or in resistance to one or more environmental stresses,such that the yields or rate of production of a desired fine chemical bythis microorganism is improved. The agent which modulates SRT proteinactivity can be an agent which stimulates SRT protein activity or SRTnucleic acid expression. Examples of agents which stimulate SRT proteinactivity or SRT nucleic acid expression include small molecules, activeSRT proteins, and nucleic acids encoding SRT proteins that have beenintroduced into the cell. Examples of agents which inhibit SRT activityor expression include small molecules, and antisense SRT nucleic acidmolecules.

Another aspect of the invention pertains to methods for modulatingyields of a desired compound from a cell, involving the introduction ofa wild-type or mutant SRT gene into a cell, either maintained on aseparate plasmid or integrated into the genome of the host cell. Ifintegrated into the genome, such integration can random, or it can takeplace by homologous recombination such that the native gene is replacedby the introduced copy, causing the production of the desired compoundfrom the cell to be modulated. In a preferred embodiment, said yieldsare increased. In another preferred embodiment, said chemical is a finechemical. In a particularly preferred embodiment, said fine chemical isan amino acid. In especially preferred embodiments, said amino acid isL-lysine.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides SRT nucleic acid and protein moleculeswhich are involved in the survival of C. glutamicum upon exposure ofthis microorganism to chemical or environmental hazards. The moleculesof the invention may be utilized in the modulation of production of finechemicals from microorganisms, since these SRT proteins provide a meansfor continued growth and multiplication of C. glutamicum in the presenceof toxic chemicals or hazardous environmental conditions, such as may beencountered during large-scale fermentative growth. By increasing thegrowth rate or at least maintaining normal growth in the face of poor,if not toxic, conditions, one may increase the yield, production, and/orefficiency of production of one or more fine chemicals from such aculture, at least due to the relatively greater number of cellsproducing the fine chemical in the culture. Aspects of the invention arefurther explicated below.

I. Fine Chemicals

The term ‘fine chemical’ is art-recognized and includes moleculesproduced by an organism which have applications in various industries,such as, but not limited to, the pharmaceutical, agriculture, andcosmetics industries. Such compounds include organic acids, such astartaric acid, itaconic acid, and diaminopimelic acid, bothproteinogenic and non-proteinogenic amino acids, purine and pyrimidinebases, nucleosides, and nucleotides (as described e.g. in Kuninaka, A.(1996) Nucleotides and related compounds, p. 561-612, in Biotechnologyvol. 6, Rehm et al., eds. VCH: Weinheim, and references containedtherein), lipids, both saturated and unsaturated fatty acids (e.g.,arachidonic acid), diols (e.g., propane diol, and butane diol),carbohydrates (e.g., hyaluronic acid and trehalose), aromatic compounds(e.g., aromatic amines, vanillin, and indigo), vitamins and cofactors(as described in Ullmann's Encyclopedia of Industrial Chemistry, vol.A27, “Vitamins”, p. 443-613 (1996) VCH: Weinheim and references therein;and Ong, A. S., Niki, E. & Packer, L. (1995) “Nutrition, Lipids, Health,and Disease” Proceedings of the UNESCO/Confederation of Scientific andTechnological Associations in Malaysia, and the Society for Free RadicalResearch—Asia, held Sep. 1-3, 1994 at Penang, Malaysia, AOCS Press,(1995)), enzymes, polyketides (Cane et al. (1998) Science 282: 63-68),and all other chemicals described in Gutcho (1983) Chemicals byFermentation, Noyes Data Corporation, ISBN: 0818805086 and referencestherein. The metabolism and uses of certain of these fine chemicals arefurther explicated below.

A. Amino Acid Metabolism and Uses

Amino acids comprise the basic structural units of all proteins, and assuch are essential for normal cellular functioning in all organisms. Theterm “amino acid” is art-recognized. The proteinogenic amino acids, ofwhich there are 20 species, serve as structural units for proteins, inwhich they are linked by peptide bonds, while the nonproteinogenic aminoacids (hundreds of which are known) are not normally found in proteins(see Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p. 57-97VCH: Weinheim (1985)). Amino acids may be in the D- or L-opticalconfiguration, though L-amino acids are generally the only type found innaturally-occurring proteins. Biosynthetic and degradative pathways ofeach of the 20 proteinogenic amino acids have been well characterized inboth prokaryotic and eukaryotic cells (see, for example, Stryer, L.Biochemistry, 3^(rd) edition, pages 578-590 (1988)). The ‘essential’amino acids (histidine, isoleucine, leucine, lysine, methionine,phenylalanine, threonine, tryptophan, and valine), so named because theyare generally a nutritional requirement due to the complexity of theirbiosyntheses, are readily converted by simple biosynthetic pathways tothe remaining 11 ‘nonessential’ amino acids (alanine, arginine,asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline,serine, and tyrosine). Higher animals do retain the ability tosynthesize some of these amino acids, but the essential amino acids mustbe supplied from the diet in order for normal protein synthesis tooccur.

Aside from their function in protein biosynthesis, these amino acids areinteresting chemicals in their own right, and many have been found tohave various applications in the food, feed, chemical, cosmetics,agriculture, and pharmaceutical industries. Lysine is an important aminoacid in the nutrition not only of humans, but also of monogastricanimals such as poultry and swine. Glutamate is most commonly used as aflavor additive (mono-sodium glutamate, MSG) and is widely usedthroughout the food industry, as are aspartate, phenylalanine, glycine,and cysteine. Glycine, L-methionine and tryptophan are all utilized inthe pharmaceutical industry. Glutamine, valine, leucine, isoleucine,histidine, arginine, proline, serine and alanine are of use in both thepharmaceutical and cosmetics industries. Threonine, tryptophan, andD/L-methionine are common feed additives. (Leuchtenberger, W. (1996)Amino aids—technical production and use, p. 466-502 in Rehm et al (eds.)Biotechnology vol. 6, chapter 14a, VCH: Weinheim). Additionally, theseamino acids have been found to be useful as precursors for the synthesisof synthetic amino acids and proteins, such as N-acetylcysteine,S-carboxymethyl-L-cysteine, (S)-5-hydroxytryptophan, and othersdescribed in Ulmann's Encyclopedia of Industrial Chemistry, vol. A2, p.57-97, VCH: Weinheim, 1985.

The biosynthesis of these natural amino acids in organisms capable ofproducing them, such as bacteria, has been well characterized (forreview of bacterial amino acid biosynthesis and regulation thereof, seeUmbarger, H. E. (1978) Ann. Rev. Biochem. 47: 533-606). Glutamate issynthesized by the reductive amination of α-ketoglutarate, anintermediate in the citric acid cycle. Glutamine, proline, and arginineare each subsequently produced from glutamate. The biosynthesis ofserine is a three-step process beginning with 3-phosphoglycerate (anintermediate in glycolysis), and resulting in this amino acid afteroxidation, transamination, and hydrolysis steps. Both cysteine andglycine are produced from serine; the former by the condensation ofhomocysteine with serine, and the latter by the transferal of theside-chain β-carbon atom to tetrahydrofolate, in a reaction catalyzed byserine transhydroxymethylase. Phenylalanine, and tyrosine aresynthesized from the glycolytic and pentose phosphate pathway precursorserythrose 4-phosphate and phosphoenolpyruvate in a 9-step biosyntheticpathway that differ only at the final two steps after synthesis ofprephenate. Tryptophan is also produced from these two initialmolecules, but its synthesis is an 11-step pathway. Tyrosine may also besynthesized from phenylalanine, in a reaction catalyzed by phenylalaninehydroxylase. Alanine, valine, and leucine are all biosynthetic productsof pyruvate, the final product of glycolysis. Aspartate is formed fromoxaloacetate, an intermediate of the citric acid cycle. Asparagine,methionine, threonine, and lysine are each produced by the conversion ofaspartate. Isoleucine is formed from threonine. A complex 9-step pathwayresults in the production of histidine from5-phosphoribosyl-1-pyrophosphate, an activated sugar.

Amino acids in excess of the protein synthesis needs of the cell cannotbe stored, and are instead degraded to provide intermediates for themajor metabolic pathways of the cell (for review see Stryer, L.Biochemistry 3^(rd) ed. Ch. 21 “Amino Acid Degradation and the UreaCycle” p. 495-516 (1988)). Although the cell is able to convert unwantedamino acids into useful metabolic intermediates, amino acid productionis costly in terms of energy, precursor molecules, and the enzymesnecessary to synthesize them. Thus it is not surprising that amino acidbiosynthesis is regulated by feedback inhibition, in which the presenceof a particular amino acid serves to slow or entirely stop its ownproduction (for overview of feedback mechanisms in amino acidbiosynthetic pathways, see Stryer, L. Biochemistry, 3^(rd) ed. Ch. 24:“Biosynthesis of Amino Acids and Heme” p. 575-600 (1988)). Thus, theoutput of any particular amino acid is limited by the amount of thatamino acid present in the cell.

B. Vitamin, Cofactor, and Nutraceutical Metabolism and Uses

Vitamins, cofactors, and nutraceuticals comprise another group ofmolecules which the higher animals have lost the ability to synthesizeand so must ingest, although they are readily synthesized by otherorganisms, such as bacteria. These molecules are either bioactivesubstances themselves, or are precursors of biologically activesubstances which may serve as electron carriers or intermediates in avariety of metabolic pathways. Aside from their nutritive value, thesecompounds also have significant industrial value as coloring agents,antioxidants, and catalysts or other processing aids. (For an overviewof the structure, activity, and industrial applications of thesecompounds, see, for example, Ullman's Encyclopedia of IndustrialChemistry, “Vitamins” vol. A27, p. 443-613, VCH: Weinheim, 1996.) Theterm “vitamin” is art-recognized, and includes nutrients which arerequired by an organism for normal functioning, but which that organismcannot synthesize by itself. The group of vitamins may encompasscofactors and nutraceutical compounds. The language “cofactor” includesnonproteinaceous compounds required for a normal enzymatic activity tooccur. Such compounds may be organic or inorganic; the cofactormolecules of the invention are preferably organic. The term“nutraceutical” includes dietary supplements having health benefits inplants and animals, particularly humans. Examples of such molecules arevitamins, antioxidants, and also certain lipids (e.g., polyunsaturatedfatty acids).

The biosynthesis of these molecules in organisms capable of producingthem, such as bacteria, has been largely characterized (Ullman'sEncyclopedia of Industrial Chemistry, “Vitamins” vol. A27, p. 443-613,VCH: Weinheim, 1996; Michal, G. (1999) Biochemical Pathways: An Atlas ofBiochemistry and Molecular Biology, John Wiley & Sons; Ong, A. S., Niki,E. & Packer, L. (1995) “Nutrition, Lipids, Health, and Disease”Proceedings of the UNESCO/Confederation of Scientific and TechnologicalAssociations in Malaysia, and the Society for Free RadicalResearch—Asia, held Sep. 1-3, 1994 at Penang, Malaysia, AOCS Press:Champaign, Ill. X, 374 S).

Thiamin (vitamin B₁) is produced by the chemical coupling of pyrimidineand thiazole moieties. Riboflavin (vitamin B₂) is synthesized fromguanosine-5′-triphosphate (GTP) and ribose-5′-phosphate. Riboflavin, inturn, is utilized for the synthesis of flavin mononucleotide (FMN) andflavin adenine dinucleotide (FAD). The family of compounds collectivelytermed ‘vitamin B₆’ (e.g., pyridoxine, pyridoxamine,pyridoxa-5′-phosphate, and the commercially used pyridoxinhydrochloride) are all derivatives of the common structural unit,5-hydroxy-6-methylpyridine. Pantothenate (pantothenic acid,(R)-(+)-N-(2,4-dihydroxy-3,3-dimethyl-1-oxobutyl)-β-alanine) can beproduced either by chemical synthesis or by fermentation. The finalsteps in pantothenate biosynthesis consist of the ATP-drivencondensation of β-alanine and pantoic acid. The enzymes responsible forthe biosynthesis steps for the conversion to pantoic acid, to β-alanineand for the condensation to panthotenic acid are known. Themetabolically active form of pantothenate is Coenzyme A, for which thebiosynthesis proceeds in 5 enzymatic steps. Pantothenate,pyridoxal-5′-phosphate, cysteine and ATP are the precursors of CoenzymeA. These enzymes not only catalyze the formation of panthothante, butalso the production of (R)-pantoic acid, (R)-pantolacton, (R)-panthenol(provitamin B₅), pantetheine (and its derivatives) and coenzyme A.

Biotin biosynthesis from the precursor molecule pimeloyl-CoA inmicroorganisms has been studied in detail and several of the genesinvolved have been identified. Many of the corresponding proteins havebeen found to also be involved in Fe-cluster synthesis and are membersof the nifS class of proteins. Lipoic acid is derived from octanoicacid, and serves as a coenzyme in energy metabolism, where it becomespart of the pyruvate dehydrogenase complex and the α-ketoglutaratedehydrogenase complex. The folates are a group of substances which areall derivatives of folic acid, which is turn is derived from L-glutamicacid, p-amino-benzoic acid and 6-methylpterin. The biosynthesis of folicacid and its derivatives, starting from the metabolism intermediatesguanosine-5′-triphosphate (GTP), L-glutamic acid and p-amino-benzoicacid has been studied in detail in certain microorganisms.

Corrinoids (such as the cobalamines and particularly vitamin B₁₂) andporphyrines belong to a group of chemicals characterized by atetrapyrole ring system. The biosynthesis of vitamin B₁₂ is sufficientlycomplex that it has not yet been completely characterized, but many ofthe enzymes and substrates involved are now known. Nicotinic acid(nicotinate), and nicotinamide are pyridine derivatives which are alsotermed ‘niacin’. Niacin is the precursor of the important coenzymes NAD(nicotinamide adenine dinucleotide) and NADP (nicotinamide adeninedinucleotide phosphate) and their reduced forms.

The large-scale production of these compounds has largely relied oncell-free chemical syntheses, though some of these chemicals have alsobeen produced by large-scale culture of microorganisms, such asriboflavin, Vitamin B₆, pantothenate, and biotin. Only Vitamin B₁₂ isproduced solely by fermentation, due to the complexity of its synthesis.In vitro methodologies require significant inputs of materials and time,often at great cost.

C. Purine, Pyrimidine, Nucleoside and Nucleotide Metabolism and Uses

Purine and pyrimidine metabolism genes and their corresponding proteinsare important targets for the therapy of tumor diseases and viralinfections. The language “purine” or “pyrimidine” includes thenitrogenous bases which are constituents of nucleic acids, co-enzymes,and nucleotides. The term “nucleotide” includes the basic structuralunits of nucleic acid molecules, which are comprised of a nitrogenousbase, a pentose sugar (in the case of RNA, the sugar is ribose; in thecase of DNA, the sugar is D-deoxyribose), and phosphoric acid. Thelanguage “nucleoside” includes molecules which serve as precursors tonucleotides, but which are lacking the phosphoric acid moiety thatnucleotides possess. By inhibiting the biosynthesis of these molecules,or their mobilization to form nucleic acid molecules, it is possible toinhibit RNA and DNA synthesis; by inhibiting this activity in a fashiontargeted to cancerous cells, the ability of tumor cells to divide andreplicate may be inhibited. Additionally, there are nucleotides which donot form nucleic acid molecules, but rather serve as energy stores(i.e., AMP) or as coenzymes (i.e., FAD and NAD).

Several publications have described the use of these chemicals for thesemedical indications, by influencing purine and/or pyrimidine metabolism(e.g. Christopherson, R. I. and Lyons, S. D. (1990) “Potent inhibitorsof de novo pyrimidine and purine biosynthesis as chemotherapeuticagents.” Med. Res. Reviews 10: 505-548). Studies of enzymes involved inpurine and pyrimidine metabolism have been focused on the development ofnew drugs which can be used, for example, as immunosuppressants oranti-proliferants (Smith, J. L., (1995) “Enzymes in nucleotidesynthesis.” Curr. Opin. Struct. Biol. 5: 752-757; (1995) Biochem Soc.Transact. 23: 877-902). However, purine and pyrimidine bases,nucleosides and nucleotides have other utilities: as intermediates inthe biosynthesis of several fine chemicals (e.g., thiamine,S-adenosyl-methionine, folates, or riboflavin), as energy carriers forthe cell (e.g., ATP or GTP), and for chemicals themselves, commonly usedas flavor enhancers (e.g., IMP or GMP) or for several medicinalapplications (see, for example, Kuninaka, A. (1996) Nucleotides andRelated Compounds in Biotechnology vol. 6, Rehm et al., eds. VCH:Weinheim, p. 561-612). Also, enzymes involved in purine, pyrimidine,nucleoside, or nucleotide metabolism are increasingly serving as targetsagainst which chemicals for crop protection, including fungicides,herbicides and insecticides, are developed.

The metabolism of these compounds in bacteria has been characterized(for reviews see, for example, Zalkin, H. and Dixon, J. E. (1992) “denovo purine nucleotide biosynthesis”, in: Progress in Nucleic AcidResearch and Molecular Biology, vol. 42, Academic Press: p. 259-287; andMichal, G. (1999) “Nucleotides and Nucleosides”, Chapter 8 in:Biochemical Pathways: An Atlas of Biochemistry and Molecular Biology,Wiley: New York). Purine metabolism has been the subject of intensiveresearch, and is essential to the normal functioning of the cell.Impaired purine metabolism in higher animals can cause severe disease,such as gout. Purine nucleotides are synthesized fromribose-5-phosphate, in a series of steps through the intermediatecompound inosine-5′-phosphate (IMP), resulting in the production ofguanosine-5′-monophosphate (GMP) or adenosine-5′-monophosphate (AMP),from which the triphosphate forms utilized as nucleotides are readilyformed. These compounds are also utilized as energy stores, so theirdegradation provides energy for many different biochemical processes inthe cell. Pyrimidine biosynthesis proceeds by the formation ofuridine-5′-monophosphate (UMP) from ribose-5-phosphate. UMP, in turn, isconverted to cytidine-5′-triphosphate (CTP). The deoxy-forms of all ofthese nucleotides are produced in a one step reduction reaction from thediphosphate ribose form of the nucleotide to the diphosphate deoxyriboseform of the nucleotide. Upon phosphorylation, these molecules are ableto participate in DNA synthesis.

D. Trehalose Metabolism and Uses

Trehalose consists of two glucose molecules, bound in α, α-1,1 linkage.It is commonly used in the food industry as a sweetener, an additive fordried or frozen foods, and in beverages. However, it also hasapplications in the pharmaceutical, cosmetics and biotechnologyindustries (see, for example, Nishimoto et al., (1998) U.S. Pat. No.5,759,610; Singer, M. A. and Lindquist, S. (1998) Trends Biotech. 16:460-467; Paiva, C. L. A. and Panek, A. D. (1996) Biotech. Ann. Rev. 2:293-314; and Shiosaka, M. (1997) J. Japan 172: 97-102). Trehalose isproduced by enzymes from many microorganisms and is naturally releasedinto the surrounding medium, from which it can be collected usingmethods known in the art.

II. Resistance to Damage from Chemicals Environmental Stress, andAntibiotics

Production of fine chemicals is typically performed by large-scaleculture of bacteria developed to produce and secrete large quantities ofthese molecules. However, this type of large-scale fermentation resultsin the subjection of the microorganisms to stresses of various kinds.These stresses include environmental stress and chemical stress.

A. Resistance to Environmental Stress

Examples of environmental stresses typically encountered in large-scalefermentative culture include mechanical stress, heat stress, stress dueto limited oxygen, stress due to oxygen radicals, pH stress, and osmoticstress. The stirring mechanism used in most large-scale fermentors toensure aeration of the culture produces heat, thus increasing thetemperature of the culture. Increases in temperature induce thewell-characterized heat shock response, in which a set of proteins areexpressed which not only aid in the survival of the bacterium in theface of high temperatures, but also increase survival in response to anumber of other environmental stresses (see Neidhardt, F. C., et al.,eds. (1996) E. coli and Salmonella. ASM Press: Washington, D.C., p.1382-1399; Wosten, M. M. (1998) FEMS Microbiology Reviews 22(3): 127-50;Bahl, H. et al. (1995) FEMS Microbiology Reviews 17(3): 341-348;Zimmerman, J. L., Cohill, P. R. (1991) New Biologist 3(7): 641-650;Samali, A., and Orrenius, S. (1998) Cell. Stress Chaperones 3(4):228-236, and references contained therein from each of these citations).Regulation of the heat shock response in bacteria is facilitated byspecific sigma factors and other cellular regulators of gene expression(Hecker, M., Volker, U (1998). Molecular Microbiology 29(5): 1129-1136).One of the largest problems that the cell encounters when exposed tohigh temperature is that protein folding is impaired; nascent proteinshave sufficient kinetic energy in high temperature circumstances that itis difficult for the growing polypeptide chain to remain in a stableconformation long enough to fold properly. Thus, two of the key types ofproteins expressed during the heat shock response consist of chaperones(proteins which assist in the folding or unfolding of otherproteins—see, e.g., Fink, A. L. (1999) Physiol. Rev. 79(2): 425-449),and proteases, which can destroy any improperly folded proteins.Examples of chaperones expressed during the heat shock response includeGroEL and DNAK; proteases known to be expressed during this cellularreaction to heat shock include Lon, FtsH, and ClpB.

Other environmental stresses besides heat may also provoke a stressresponse. Though the fermentor stirring process is meant to introduceoxygen into the culture, oxygen may remain in limited supply,particularly when the culture is advanced in growth and the oxygen needsof the culture are thereby increased; an insufficient supply of oxygenis another stress for the microorganism. Cells in fermentor cultures arealso subjected to a number of osmotic stresses, particularly whennutrients are added to the culture, resulting in a high extracellularand low intracellular concentration of these molecules. Further, thelarge quantities of the desired molecules produced by these organisms inculture may contribute to osmotic stress of the bacteria. Lastly,aerobic metabolism such as that used by C. glutamicum results in carbondioxide as a waste product; secretion of this molecule may acidify theculture medium due to conversion of this molecule to carboxylic acid.Thus, bacteria in culture are also frequently subjected to acidic pHstress. The converse may also be true—when high levels of basic wastemolecules such as ammonium are present in the culture medium, thebacteria in culture may be subjected to basic pH stress as well.

To combat such environmental stresses, bacteria have elegant genesystems which are expressed upon exposure to one or more stresses, suchas the aforementioned heat shock system. Genes expressed in response toosmotic stress, for example, encode proteins capable of transporting orsynthesizing compatible solutes such that osmotic intake or export of aparticular molecule is slowed to manageable levels. Other examples ofstress-induced bacterial proteins are those involved in trehalosebiosynthesis, those encoding enzymes involved in ppGpp metabolism, thoseinvolved in signal transduction, particularly those encodingtwo-component systems which are sensitive to osmotic pressure, and thoseencoding transcription factors which are responsive to a variety ofstress factors (e.g., RssB analogues and/or sigma factors). Many othersuch genes and their protein products are known in the art.

B. Resistance to Chemical Stress

Aside from environmental stresses, cells may also experience a number ofchemical stresses. These may fall into two categories. The first arenatural waste products of metabolism and other cellular processes whichare secreted by the cell to the surrounding medium. The second arechemicals present in the extracellular medium which do not originatefrom the cell. Generally, when cells excrete toxic waste products fromthe concentrated intracellular cytoplasm into the relatively much moredilute extracellular medium, these products dissipate such thatextracellular levels of the possibly toxic compound are quite low.However, in large-scale fermentative culture of the bacterium, this maynot be the case: so many bacteria are grown in a relatively smallenvironment and at such a high metabolic rate that waste products mayaccumulate in the medium to nearly toxic levels. Examples of such wastesare carbon dioxide, metal ions, and reactive oxygen species such ashydrogen peroxide. These compounds may interfere with the activity orstructure of cell surface molecules, or may re-enter the cell, wherethey can seriously damage proteins and nucleic acids alike. Certainother chemicals hazardous to the normal functioning of cells may benaturally found in the extracellular medium. For example, metal ionssuch as mercury, cadmium, nickel or copper are frequently found in watersources, and may form tight complexes with cellular enzymes whichprevent the normal functioning of these proteins.

C. Resistance to Antibiotics

Bacteriocidal proteins or antibiotics, may also be found in theextracellular milieu, either through the intervention of the researcher,or as a natural product from another organism, utilized to gain acompetitive advantage. Microorganisms have several art-known mechanismsto protect themselves against antimicrobial chemicals. Degradation,modification, and export of compounds toxic to the cell are commonmethods by which microorganisms eliminate or detoxify antibiotics.Cytoplasmic ‘efflux-pumps’ are known in several prokaryotes and showsimilarities to the so-called ‘multidrug resistance’ proteins fromhigher eukaryotes (Neyfakh, A. A., et al. (1991) Proc. Natl. Acad. Sci.USA 88: 4781-4785). Examples of such proteins include emrAB from E. coli(Lomovskaya, O. and K. Lewis (1992) Proc. Natl. Acad. Sci. USA 89:8938-8942), lmrB from B. subtilis (Kumano, M. et al. (1997) Microbiology143: 2775-2782), smr from S. aureus (Grinius, L. G. et al. (1992)Plasmid 27: 119-129) or cmr from C. glutamicum (Kaidoh, K. et al. (1997)Micro. Drug Resist. 3: 345-350). C. glutamicum itself is non-pathogenic,in contrast to several other members of the genus Corynebacterium, suchas C. diphtheriae or C. pseudotuberculosis. Several pathogenicCorynebacteria are known to have multiple resistances against a varietyof antibiotics, such as C. jeikeium and C. urealyticum (Soriano, F. etal. (1995) Antimicrob. Agents Chemother. 39: 208-214).

Lincosamides are recognized as effective antibiotics againstCorynebacterium species (Soriano, F. et al. (1995) Antimicrob. AgentsChemother. 39: 208-214). An unexpected result of the present inventionwas the identification of a gene encoding a lincosamide-resistanceprotein (in particular, a lincomycin-resistance protein). The LMRBprotein from C. glutamicum shows 40% homology to the product of the lmrBgene from B. subtilis (see Genbank accession no. AL009126), ascalculated using version 1.7 of the program CLUSTALW (Thompson, J. D.,Higgins, D. G., Gibson, T. J. (1994) Nucl. Acids Res. 22: 4673-4680)using standard parameters (PAIRWISE ALIGNMENT PARAMETERS: slow/accuratealignments: Gap Open Penalty=10.00 Gap Extension Penalty=0.10, Proteinweight matrix=BLOSUM 30, DNA weight matrix=IUB, Fast/Approximatealignments: Gap penalty=3, K-tuple (word) size=1, No. of topdiagonals=5, Window size=5, Toggle Slow/Fast pairwise alignments=slow.Multiple alignment parameters: Gap Opening Penalty=10.00, Gap ExtensionPenalty=0.05, Delay divergent sequences=40%, DNA transitionsweight=0.50, Protein weight matrix=BLOSUM series, DNA weight matrix=IUB,Use negative matrix=OFF).

Environmental stress, chemical stress, and antibiotic or otherantimicrobial stress may influence the behavior of the microorganismsduring fermentor culture, and may have an impact on the production ofthe desired compound from these organisms. For example, osmotic stressof a microorganism may cause inappropriate or inappropriately rapiduptake of one or more compounds which can ultimately lead to cellulardamage or death due to osmotic shock. Similarly, chemicals present inthe culture, either exogenously added (e.g., antimicrobial compoundsintended to eliminate unwanted microbes) or generated by the bacteriathemselves (e.g., waste compounds such as heavy metals or oxygenradicals, or even antimicrobial compounds) may result in inhibition offine chemical production or even death of the organism. The genes of theinvention encode C. glutamicum proteins which act to prevent cell damageor death, by specifically counteracting the source or effect of theenvironmental or chemical stress.

III. Elements and Methods of the Invention

The present invention is based, at least in part, on the discovery ofnovel molecules, referred to herein as SRT nucleic acid and proteinmolecules, which increase the ability of C. glutamicum to survive inchemically or environmentally hazardous settings. In one embodiment, theSRT molecules function to confer resistance to one or more environmentalor chemical stresses to C. glutamicum. In a preferred embodiment, theactivity of the SRT molecules of the present invention has an impact onthe production of a desired fine chemical by this organism. In aparticularly preferred embodiment, the SRT molecules of the inventionare modulated in activity, such that the yield, production, and/orefficiency of production of one or more fine chemicals from C.glutamicum is also modulated.

The language, “SRT protein” or “SRT polypeptide” includes proteins whichparticipate in the resistance of C. glutamicum to one or moreenvironmental or chemical stresses. Examples of SRT proteins includethose encoded by the SRT genes set forth in Table 1 and Appendix A. Theterms “SRT gene” or “SRT nucleic acid sequence” include nucleic acidsequences encoding an SRT protein, which consist of a coding region andalso corresponding untranslated 5′ and 3′ sequence regions. Examples ofSRT genes include those set forth in Table 1. The terms “production” or“productivity” are art-recognized and include the concentration of thefermentation product (for example, the desired fine chemical) formedwithin a given time and a given fermentation volume (e.g., kg productper hour per liter). The term “efficiency of production” includes thetime required for a particular level of production to be achieved (forexample, how long it takes for the cell to attain a particular rate ofoutput of a fine chemical). The term “yield” or “product/carbon yield”is art-recognized and includes the efficiency of the conversion of thecarbon source into the product (i.e., fine chemical). This is generallywritten as, for example, kg product per kg carbon source. By increasingthe yield or production of the compound, the quantity of recoveredmolecules, or of useful recovered molecules of that compound in a givenamount of culture over a given amount of time is increased. The terms“biosynthesis” or a “biosynthetic pathway” are art-recognized andinclude the synthesis of a compound, preferably an organic compound, bya cell from intermediate compounds in what may be a multistep and highlyregulated process. The terms “degradation” or a “degradation pathway”are art-recognized and include the breakdown of a compound, preferablyan organic compound, by a cell to degradation products (generallyspeaking, smaller or less complex molecules) in what may be a multistepand highly regulated process. The language “metabolism” isart-recognized and includes the totality of the biochemical reactionsthat take place in an organism. The metabolism of a particular compound,then, (e.g., the metabolism of an amino acid such as glycine) comprisesthe overall biosynthetic, modification, and degradation pathways in thecell related to this compound. The terms “resistance” and “tolerance”are art-known and include the ability of a cell to not be affected byexposure to a chemical or an environment which would otherwise bedetrimental to the normal functioning of these organisms. The terms“stress” or “hazard” include factors which are detrimental to the normalfunctioning of cells such as C. glutamicum. Examples of stresses include“chemical stress”, in which a cell is exposed to one or more chemicalswhich are detrimental to the cell, and “environmental stress” where acell is exposed to an environmental condition outside of those to whichit is adapted. Chemical stresses may be either natural metabolic wasteproducts such as, but not limited to reactive oxygen species or carbondioxide, or chemicals otherwise present in the environment, including,but not limited to heavy metal ions or bacteriocidal proteins such asantibiotics. Environmental stresses may be, but are not limited totemperatures outside of the normal range, suboptimal oxygenavailability, osmotic pressures, or extremes of pH, for example.

In another embodiment, the SRT molecules of the invention are capable ofmodulating the production of a desired molecule, such as a finechemical, in a microorganism such as C. glutamicum. Using recombinantgenetic techniques, one or more of the SRT proteins of the invention maybe manipulated such that its function is modulated. The alteration ofactivity of stress response, resistance or tolerance genes such that thecell is increased in tolerance to one or more stresses may improve theability of that cell to grow and multiply in the relatively stressfulconditions of large-scale fermentor culture. For example, byoverexpressing or engineering a heat-shock induced chaperone moleculesuch that it is optimized in activity, one may increase the ability ofthe bacterium to correctly fold proteins in the face of nonoptimaltemperature conditions. By having fewer misfolded (and possiblymisregulated or nonfunctional) proteins, the cell is increased in itsability to function normally in such a culture, which should in turnprovide increased viability. This overall increase in number of cellshaving greater viability and activity in the culture should also resultin an increase in the yield, production, and/or efficiency of productionof one or more desired fine chemicals, due at least to the relativelygreater number of cells producing these chemicals in the culture.

The isolated nucleic acid sequences of the invention are containedwithin the genome of a Corynebacterium glutamicum strain availablethrough the American Type Culture Collection, given designation ATCC13032. The nucleotide sequence of the isolated C. glutamicum SRT DNAsand the predicted amino acid sequences of the C. glutamicum SRT proteinsare shown in Appendices A and B, respectively. Computational analyseswere performed which classified and/or identified these nucleotidesequences as sequences which encode chemical and environmental stress,resistance, and tolerance proteins.

The present invention also pertains to proteins which have an amino acidsequence which is substantially homologous to an amino acid sequence ofAppendix B. As used herein, a protein which has an amino acid sequencewhich is substantially homologous to a selected amino acid sequence isleast about 50% homologous to the selected amino acid sequence, e.g.,the entire selected amino acid sequence. A protein which has an aminoacid sequence which is substantially homologous to a selected amino acidsequence can also be least about 50-60%, preferably at least about60-70%, and more preferably at least about 70-80%, 80-90%, or 90-95%,and most preferably at least about 96%, 97%, 98%, 99% or more homologousto the selected amino acid sequence. Ranges and identity valuesintermediate to the above-recited values, (e.g., 75%-80% identical,85-87% identical, 91-92% identical) are also intended to be encompassedby the present invention. For example, ranges of identity values using acombination of any of the above values recited as upper and/or lowerlimits are intended to be included.

The SRT proteins or biologically active portions or fragments thereof ofthe invention can confer resistance or tolerance to one or more chemicalor environmental stresses, or may have one or more of the activities setforth in Table 1.

Various aspects of the invention are described in further detail in thefollowing subsections:

A. Isolated Nucleic Acid Molecules

One aspect of the invention pertains to isolated nucleic acid moleculesthat encode SRT polypeptides or biologically active portions thereof, aswell as nucleic acid fragments sufficient for use as hybridizationprobes or primers for the identification or amplification ofSRT-encoding nucleic acid (e.g., SRT DNA). As used herein, the term“nucleic acid molecule” is intended to include DNA molecules (e.g., cDNAor genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA orRNA generated using nucleotide analogs. This term also encompassesuntranslated sequence located at both the 3′ and 5′ ends of the codingregion of the gene: at least about 100 nucleotides of sequence upstreamfrom the 5′ end of the coding region and at least about 20 nucleotidesof sequence downstream from the 3′end of the coding region of the gene.The nucleic acid molecule can be single-stranded or double-stranded, butpreferably is double-stranded DNA. An “isolated” nucleic acid moleculeis one which is separated from other nucleic acid molecules which arepresent in the natural source of the nucleic acid. Preferably, an“isolated” nucleic acid is free of sequences which naturally flank thenucleic acid (i.e., sequences located at the 5′ and 3′ ends of thenucleic acid) in the genomic DNA of the organism from which the nucleicacid is derived. For example, in various embodiments, the isolated SRTnucleic acid molecule can contain less than about 5 kb, 4 kb, 3 kb, 2kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flankthe nucleic acid molecule in genomic DNA of the cell from which thenucleic acid is derived (e.g, a C. glutamicum cell). Moreover, an“isolated” nucleic acid molecule, such as a DNA molecule, can besubstantially free of other cellular material, or culture medium whenproduced by recombinant techniques, or chemical precursors or otherchemicals when chemically synthesized.

A nucleic acid molecule of the present invention, e.g., a nucleic acidmolecule having a nucleotide sequence of Appendix A, or a portionthereof, can be isolated using standard molecular biology techniques andthe sequence information provided herein. For example, a C. glutamicumSRT DNA can be isolated from a C. glutamicum library using all orportion of one of the sequences of Appendix A as a hybridization probeand standard hybridization techniques (e.g., as described in Sambrook,J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A LaboratoryManual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1989). Moreover, a nucleicacid molecule encompassing all or a portion of one of the sequences ofAppendix A can be isolated by the polymerase chain reaction usingoligonucleotide primers designed based upon this sequence (e.g., anucleic acid molecule encompassing all or a portion of one of thesequences of Appendix A can be isolated by the polymerase chain reactionusing oligonucleotide primers designed based upon this same sequence ofAppendix A). For example, mRNA can be isolated from normal endothelialcells (e.g., by the guanidinium-thiocyanate extraction procedure ofChirgwin et al. (1979) Biochemistry 18: 5294-5299) and DNA can beprepared using reverse transcriptase (e.g., Moloney MLV reversetranscriptase, available from Gibco/BRL, Bethesda, Md.; or AMV reversetranscriptase, available from Seikagaku America, Inc., St. Petersburg,Fla.). Synthetic oligonucleotide primers for polymerase chain reactionamplification can be designed based upon one of the nucleotide sequencesshown in Appendix A. A nucleic acid of the invention can be amplifiedusing cDNA or, alternatively, genomic DNA, as a template and appropriateoligonucleotide primers according to standard PCR amplificationtechniques. The nucleic acid so amplified can be cloned into anappropriate vector and characterized by DNA sequence analysis.Furthermore, oligonucleotides corresponding to an SRT nucleotidesequence can be prepared by standard synthetic techniques, e.g., usingan automated DNA synthesizer.

In a preferred embodiment, an isolated nucleic acid molecule of theinvention comprises one of the nucleotide sequences shown in Appendix A.The sequences of Appendix A correspond to the Corynebacterium glutamicumSRT DNAs of the invention. This DNA comprises sequences encoding SRTproteins (i.e., the “coding region”, indicated in each sequence inAppendix A), as well as 5′ untranslated sequences and 3′ untranslatedsequences, also indicated in Appendix A. Alternatively, the nucleic acidmolecule can comprise only the coding region of any of the sequences inAppendix A.

For the purposes of this application, it will be understood that each ofthe sequences set forth in Appendix A has an identifying RXA, RXN, orRXSnumber having the designation “RXA”, “RXN”, or “RXS” followed by 5digits (i.e., RXA01524, RXN00493, or RXS01027). Each of these sequencescomprises up to three parts: a 5′ upstream region, a coding region, anda downstream region. Each of these three regions is identified by thesame RXA, RXN, or RXS designation to eliminate confusion. The recitation“one of the sequences in Appendix A”, then, refers to any of thesequences in Appendix A, which may be distinguished by their differingRXA, RXN, or RXS designations. The coding region of each of thesesequences is translated into a corresponding amino acid sequence, whichis set forth in Appendix B. The sequences of Appendix B are identifiedby the same RXA, RXN, or RXS designations as Appendix A, such that theycan be readily correlated. For example, the amino acid sequence inAppendix B designated RXA01524 is a translation of the coding region ofthe nucleotide sequence of nucleic acid molecule RXA01524 in Appendix A,the amino acid sequence in Appendix B designated RXN00034 is atranslation of the coding region of the nucleotide sequence of nucleicacid molecule RXN00034 in Appendix A, and the amino acid sequence inAppendix B designated RXS00568 is a translation of the coding region ofthe nucleotide sequence of nucleic acid molecule RXS00568 in Appendix A.Each of the RXA, RXN, and RXS nucleotide and amino acid sequences of theinvention has also been assigned a SEQ ID NO, as indicated in Table 1.

Several of the genes of the invention are “F-designated genes”. AnF-designated gene includes those genes set forth in Table 1 which havean ‘F’ in front of the RXA, RXN, or RXS designation. For example, SEQ IDNO:7, designated, as indicated on Table 1, as “F RXA00498”, is anF-designated gene, as are SEQ ID NOs: 25, 33, and 37 (designated onTable 1 as “F RXA01345”, “F RXA02543”, and “F RXA02282”, respectively).

In one embodiment, the nucleic acid molecules of the present inventionare not intended to include those compiled in Table 2. In the case ofthe dapD gene, a sequence for this gene was published in Wehrmann, A.,et al. (1998) J. Bacteriol. 180(12): 3159-3165. However, the sequenceobtained by the inventors of the present application is significantlylonger than the published version. It is believed that the publishedversion relied on an incorrect start codon, and thus represents only afragment of the actual coding region.

In another preferred embodiment, an isolated nucleic acid molecule ofthe invention comprises a nucleic acid molecule which is a complement ofone of the nucleotide sequences shown in Appendix A, or a portionthereof. A nucleic acid molecule which is complementary to one of thenucleotide sequences shown in Appendix A is one which is sufficientlycomplementary to one of the nucleotide sequences shown in Appendix Asuch that it can hybridize to one of the nucleotide sequences shown inAppendix A, thereby forming a stable duplex.

In still another preferred embodiment, an isolated nucleic acid moleculeof the invention comprises a nucleotide sequence which is at least about50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably atleast about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%%, morepreferably at least about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%,or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%,92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%,98%, 99% or more homologous to a nucleotide sequence shown in AppendixA, or a portion thereof. Ranges and identity values intermediate to theabove-recited ranges, (e.g., 70-90% identical or 80-95% identical) arealso intended to be encompassed by the present invention. For example,ranges of identity values using a combination of any of the above valuesrecited as upper and/or lower limits are intended to be included. In anadditional preferred embodiment, an isolated nucleic acid molecule ofthe invention comprises a nucleotide sequence which hybridizes, e.g.,hybridizes under stringent conditions, to one of the nucleotidesequences shown in Appendix A, or a portion thereof.

Moreover, the nucleic acid molecule of the invention can comprise only aportion of the coding region of one of the sequences in Appendix A, forexample a fragment which can be used as a probe or primer or a fragmentencoding a biologically active portion of an SRT protein. The nucleotidesequences determined from the cloning of the SRT genes from C.glutamicum allows for the generation of probes and primers designed foruse in identifying and/or cloning SRT homologues in other cell types andorganisms, as well as SRT homologues from other Corynebacteria orrelated species. The probe/primer typically comprises substantiallypurified oligonucleotide. The oligonucleotide typically comprises aregion of nucleotide sequence that hybridizes under stringent conditionsto at least about 12, preferably about 25, more preferably about 40, 50or 75 consecutive nucleotides of a sense strand of one of the sequencesset forth in Appendix A, an anti-sense sequence of one of the sequencesset forth in Appendix A, or naturally occurring mutants thereof. Primersbased on a nucleotide sequence of Appendix A can be used in PCRreactions to clone SRT homologues. Probes based on the SRT nucleotidesequences can be used to detect transcripts or genomic sequencesencoding the same or homologous proteins. In preferred embodiments, theprobe further comprises a label group attached thereto, e.g. the labelgroup can be a radioisotope, a fluorescent compound, an enzyme, or anenzyme co-factor. Such probes can be used as a part of a diagnostic testkit for identifying cells which misexpress an SRT protein, such as bymeasuring a level of an SRT-encoding nucleic acid in a sample of cells,e.g., detecting SRT mRNA levels or determining whether a genomic SRTgene has been mutated or deleted.

In one embodiment, the nucleic acid molecule of the invention encodes aprotein or portion thereof which includes an amino acid sequence whichis sufficiently homologous to an amino acid sequence of Appendix B suchthat the protein or portion thereof maintains the ability to conferresistance or tolerance of C. glutamicum to one or more chemical orenvironmental stresses. As used herein, the language “sufficientlyhomologous” refers to proteins or portions thereof which have amino acidsequences which include a minimum number of identical or equivalent(e.g., an amino acid residue which has a similar side chain as an aminoacid residue in one of the sequences of Appendix B) amino acid residuesto an amino acid sequence of Appendix B such that the protein or portionthereof is capable of participating in the resistance of C. glutamicumto one or more chemical or environmental stresses. Protein members ofsuch metabolic pathways, as described herein, function to increase theresistance or tolerance of C. glutamicum to one or more environmental orchemical hazards or stresses. Examples of such activities are alsodescribed herein. Thus, “the function of an SRT protein” contributes tothe overall resistance of C. glutamicum to elements of its surroundingswhich may impede its normal growth or functioning, and/or contributes,either directly or indirectly, to the yield, production, and/orefficiency of production of one or more fine chemicals. Examples of SRTprotein activities are set forth in Table 1.

In another embodiment, the protein is at least about 50-60%, preferablyat least about 60-70%, and more preferably at least about 70-80%,80-90%, 90-95%, and most preferably at least about 96%, 97%, 98%, 99% ormore homologous to an entire amino acid sequence of Appendix B. Rangesand identity values intermediate to the above-recited values, (e.g.,75%-80% identical, 85-87% identical, or 91-92% identical) are alsointended to be encompassed by the present invention. For example, rangesof identity values using a combination of any of the above valuesrecited as upper and/or lower limits are intended to be included.

Portions of proteins encoded by the SRT nucleic acid molecules of theinvention are preferably biologically active portions of one of the SRTproteins. As used herein, the term “biologically active portion of anSRT protein” is intended to include a portion, e.g., a domain/motif, ofan SRT protein that is capable of imparting resistance or tolerance toone or more environmental or chemical stresses or hazards, or has anactivity as set forth in Table 1. To determine whether an SRT protein ora biologically active portion thereof can increase the resistance ortolerance of C. glutamicum to one or more chemical or environmentalstresses or hazards, an assay of enzymatic activity may be performed.Such assay methods are well known to those of ordinary skill in the art,as detailed in Example 8 of the Exemplification.

Additional nucleic acid fragments encoding biologically active portionsof an SRT protein can be prepared by isolating a portion of one of thesequences in Appendix B, expressing the encoded portion of the SRTprotein or peptide (e.g., by recombinant expression in vitro) andassessing the activity of the encoded portion of the SRT protein orpeptide.

The invention further encompasses nucleic acid molecules that differfrom one of the nucleotide sequences shown in Appendix A (and portionsthereof) due to degeneracy of the genetic code and thus encode the sameSRT protein as that encoded by the nucleotide sequences shown inAppendix A. In another embodiment, an isolated nucleic acid molecule ofthe invention has a nucleotide sequence encoding a protein having anamino acid sequence shown in Appendix B. In a still further embodiment,the nucleic acid molecule of the invention encodes a full length C.glutamicum protein which is substantially homologous to an amino acidsequence of Appendix B (encoded by an open reading frame shown inAppendix A).

It will be understood by one of ordinary skill in the art that in oneembodiment the sequences of the invention are not meant to include thesequences of the prior art, such as those Genbank sequences set forth inTables 2 or 4 which were available prior to the present invention. Inone embodiment, the invention includes nucleotide and amino acidsequences having a percent identity to a nucleotide or amino acidsequence of the invention which is greater than that of a sequence ofthe prior art (e.g., a Genbank sequence (or the protein encoded by sucha sequence) set forth in Tables 2 or 4). For example, the inventionincludes a nucleotide sequence which is greater than and/or at least 39%identical to the nucleotide sequence designated RXA00084 (SEQ IDNO:189), a nucleotide sequence which is greater than and/or at least 56%identical to the nucleotide sequence designated RXA00605 (SEQ ID NO:11),and a nucleotide sequence which is greater than and/or at least 50%identical to the nucleotide sequence designated RXA00886 (SEQ ID NO:39).One of ordinary skill in the art would be able to calculate the lowerthreshold of percent identity for any given sequence of the invention byexamining the GAP-calculated percent identity scores set forth in Table4 for each of the three top hits for the given sequence, and bysubtracting the highest GAP-calculated percent identity from 100percent. One of ordinary skill in the art will also appreciate thatnucleic acid and amino acid sequences having percent identities greaterthan the lower threshold so calculated (e.g., at least 50%, 51%, 52%,53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably atleast about 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%,82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%,and even more preferably at least about 95%, 96%, 97%, 98%, 99% or moreidentical) are also encompassed by the invention.

In addition to the C. glutamicum SRT nucleotide sequences shown inAppendix A, it will be appreciated by one of ordinary skill in the artthat DNA sequence polymorphisms that lead to changes in the amino acidsequences of SRT proteins may exist within a population (e.g., the C.glutamicum population). Such genetic polymorphism in the SRT gene mayexist among individuals within a population due to natural variation. Asused herein, the terms “gene” and “recombinant gene” refer to nucleicacid molecules comprising an open reading frame encoding an SRT protein,preferably a C. glutamicum SRT protein. Such natural variations cantypically result in 1-5% variance in the nucleotide sequence of the SRTgene. Any and all such nucleotide variations and resulting amino acidpolymorphisms in SRT that are the result of natural variation and thatdo not alter the functional activity of SRT proteins are intended to bewithin the scope of the invention.

Nucleic acid molecules corresponding to natural variants and non-C.glutamicum homologues of the C. glutamicum SRT DNA of the invention canbe isolated based on their homology to the C. glutamicum SRT nucleicacid disclosed herein using the C. glutamicum DNA, or a portion thereof,as a hybridization probe according to standard hybridization techniquesunder stringent hybridization conditions. Accordingly, in anotherembodiment, an isolated nucleic acid molecule of the invention is atleast 15 nucleotides in length and hybridizes under stringent conditionsto the nucleic acid molecule comprising a nucleotide sequence ofAppendix A. In other embodiments, the nucleic acid is at least 30, 50,100, 250 or more nucleotides in length. As used herein, the term“hybridizes under stringent conditions” is intended to describeconditions for hybridization and washing under which nucleotidesequences at least 60% homologous to each other typically remainhybridized to each other. Preferably, the conditions are such thatsequences at least about 65%, more preferably at least about 70%, andeven more preferably at least about 75% or more homologous to each othertypically remain hybridized to each other. Such stringent conditions areknown to those of ordinary skill in the art in the art and can be foundin Ausubel et al., Current Protocols in Molecular Biology, John Wiley &Sons, N.Y. (1989), 6.3.1-6.3.6. A preferred, non-limiting example ofstringent hybridization conditions are hybridization in 6× sodiumchloride/sodium citrate (SSC) at about 45° C., followed by one or morewashes in 0.2×SSC, 0.1% SDS at 50-65° C. Preferably, an isolated nucleicacid molecule of the invention that hybridizes under stringentconditions to a sequence of Appendix A corresponds to anaturally-occurring nucleic acid molecule. As used herein, a“naturally-occurring” nucleic acid molecule refers to an RNA or DNAmolecule having a nucleotide sequence that occurs in nature (e.g.,encodes a natural protein). In one embodiment, the nucleic acid encodesa natural C. glutamicum SRT protein.

In addition to naturally-occurring variants of the SRT sequence that mayexist in the population, one of ordinary skill in the art will furtherappreciate that changes can be introduced by mutation into a nucleotidesequence of Appendix A, thereby leading to changes in the amino acidsequence of the encoded SRT protein, without altering the functionalability of the SRT protein. For example, nucleotide substitutionsleading to amino acid substitutions at “non-essential” amino acidresidues can be made in a sequence of Appendix A. A “non-essential”amino acid residue is a residue that can be altered from the wild-typesequence of one of the SRT proteins (Appendix B) without altering theactivity of said SRT protein, whereas an “essential” amino acid residueis required for SRT protein activity. Other amino acid residues,however, (e.g., those that are not conserved or only semi-conserved inthe domain having SRT activity) may not be essential for activity andthus are likely to be amenable to alteration without altering SRTactivity.

Accordingly, another aspect of the invention pertains to nucleic acidmolecules encoding SRT proteins that contain changes in amino acidresidues that are not essential for SRT activity. Such SRT proteinsdiffer in amino acid sequence from a sequence contained in Appendix Byet retain at least one of the SRT activities described herein. In oneembodiment, the isolated nucleic acid molecule comprises a nucleotidesequence encoding a protein, wherein the protein comprises an amino acidsequence at least about 50% homologous to an amino acid sequence ofAppendix B and is capable of increasing the resistance or tolerance ofC. glutamicum to one or more environmental or chemical stresses, or hasone or more of the activities set forth in Table 1. Preferably, theprotein encoded by the nucleic acid molecule is at least about 50-60%homologous to one of the sequences in Appendix B, more preferably atleast about 60-70% homologous to one of the sequences in Appendix B,even more preferably at least about 70-80%, 80-90%, 90-95% homologous toone of the sequences in Appendix B, and most preferably at least about96%, 97%, 98%, or 99% homologous to one of the sequences in Appendix B.

To determine the percent homology of two amino acid sequences (e.g., oneof the sequences of Appendix B and a mutant form thereof) or of twonucleic acids, the sequences are aligned for optimal comparison purposes(e.g., gaps can be introduced in the sequence of one protein or nucleicacid for optimal alignment with the other protein or nucleic acid). Theamino acid residues or nucleotides at corresponding amino acid positionsor nucleotide positions are then compared. When a position in onesequence (e.g., one of the sequences of Appendix B) is occupied by thesame amino acid residue or nucleotide as the corresponding position inthe other sequence (e.g., a mutant form of the sequence selected fromAppendix B), then the molecules are homologous at that position (i.e.,as used herein amino acid or nucleic acid “homology” is equivalent toamino acid or nucleic acid “identity”). The percent homology between thetwo sequences is a function of the number of identical positions sharedby the sequences (i.e., % homology=# of identical positions/total # ofpositions×100).

An isolated nucleic acid molecule encoding an SRT protein homologous toa protein sequence of Appendix B can be created by introducing one ormore nucleotide substitutions, additions or deletions into a nucleotidesequence of Appendix A such that one or more amino acid substitutions,additions or deletions are introduced into the encoded protein.Mutations can be introduced into one of the sequences of Appendix A bystandard techniques, such as site-directed mutagenesis and PCR-mediatedmutagenesis. Preferably, conservative amino acid substitutions are madeat one or more predicted non-essential amino acid residues. A“conservative amino acid substitution” is one in which the amino acidresidue is replaced with an amino acid residue having a similar sidechain. Families of amino acid residues having similar side chains havebeen defined in the art. These families include amino acids with basicside chains (e.g., lysine, arginine, histidine), acidic side chains(e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g.,glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine),nonpolar side chains (e.g., alanine, valine, leucine, isoleucine,proline, phenylalanine, methionine, tryptophan), beta-branched sidechains (e.g., threonine, valine, isoleucine) and aromatic side chains(e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, apredicted nonessential amino acid residue in an SRT protein ispreferably replaced with another amino acid residue from the same sidechain family. Alternatively, in another embodiment, mutations can beintroduced randomly along all or part of an SRT coding sequence, such asby saturation mutagenesis, and the resultant mutants can be screened foran SRT activity described herein to identify mutants that retain SRTactivity. Following mutagenesis of one of the sequences of Appendix A,the encoded protein can be expressed recombinantly and the activity ofthe protein can be determined using, for example, assays describedherein (see Example 8 of the Exemplification).

In addition to the nucleic acid molecules encoding SRT proteinsdescribed above, another aspect of the invention pertains to isolatednucleic acid molecules which are antisense thereto. An “antisense”nucleic acid comprises a nucleotide sequence which is complementary to a“sense” nucleic acid encoding a protein, e.g., complementary to thecoding strand of a double-stranded DNA molecule or complementary to anmRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bondto a sense nucleic acid. The antisense nucleic acid can be complementaryto an entire SRT coding strand, or to only a portion thereof. In oneembodiment, an antisense nucleic acid molecule is antisense to a “codingregion” of the coding strand of a nucleotide sequence encoding an SRTprotein. The term “coding region” refers to the region of the nucleotidesequence comprising codons which are translated into amino acid residues(e.g., the entire coding region of SEQ ID NO.: 120 (RXA00600) comprisesnucleotides 1 to 1098). In another embodiment, the antisense nucleicacid molecule is antisense to a “noncoding region” of the coding strandof a nucleotide sequence encoding SRT. The term “noncoding region”refers to 5′ and 3′ sequences which flank the coding region that are nottranslated into amino acids (i.e., also referred to as 5′ and 3′untranslated regions).

Given the coding strand sequences encoding SRT disclosed herein (e.g.,the sequences set forth in Appendix A), antisense nucleic acids of theinvention can be designed according to the rules of Watson and Crickbase pairing. The antisense nucleic acid molecule can be complementaryto the entire coding region of SRT mRNA, but more preferably is anoligonucleotide which is antisense to only a portion of the coding ornoncoding region of SRT mRNA. For example, the antisense oligonucleotidecan be complementary to the region surrounding the translation startsite of SRT mRNA. An antisense oligonucleotide can be, for example,about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length. Anantisense nucleic acid of the invention can be constructed usingchemical synthesis and enzymatic ligation reactions using proceduresknown in the art. For example, an antisense nucleic acid (e.g., anantisense oligonucleotide) can be chemically synthesized using naturallyoccurring nucleotides or variously modified nucleotides designed toincrease the biological stability of the molecules or to increase thephysical stability of the duplex formed between the antisense and sensenucleic acids, e.g., phosphorothioate derivatives and acridinesubstituted nucleotides can be used. Examples of modified nucleotideswhich can be used to generate the antisense nucleic acid include5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil,hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine,5-carboxymethylaminomethyluracil, dihydrouracil,beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine,2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine,7-methylguanine, 5-methylaminomethyluracil,5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine,5′-methoxycarboxymethyluracil, 5-methoxyuracil,2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v),wybutoxosine, pseudouracil, queosine, 2-thiocytosine,5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v),5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w,and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can beproduced biologically using an expression vector into which a nucleicacid has been subcloned in an antisense orientation (i.e., RNAtranscribed from the inserted nucleic acid will be of an antisenseorientation to a target nucleic acid of interest, described further inthe following subsection).

The antisense nucleic acid molecules of the invention are typicallyadministered to a cell or generated in situ such that they hybridizewith or bind to cellular mRNA and/or genomic DNA encoding an SRT proteinto thereby inhibit expression of the protein, e.g., by inhibitingtranscription and/or translation. The hybridization can be byconventional nucleotide complementarity to form a stable duplex, or, forexample, in the case of an antisense nucleic acid molecule which bindsto DNA duplexes, through specific interactions in the major groove ofthe double helix. The antisense molecule can be modified such that itspecifically binds to a receptor or an antigen expressed on a selectedcell surface, e.g., by linking the antisense nucleic acid molecule to apeptide or an antibody which binds to a cell surface receptor orantigen. The antisense nucleic acid molecule can also be delivered tocells using the vectors described herein. To achieve sufficientintracellular concentrations of the antisense molecules, vectorconstructs in which the antisense nucleic acid molecule is placed underthe control of a strong prokaryotic, viral, or eukaryotic promoter arepreferred.

In yet another embodiment, the antisense nucleic acid molecule of theinvention is an α-anomeric nucleic acid molecule. An α-anomeric nucleicacid molecule forms specific double-stranded hybrids with complementaryRNA in which, contrary to the usual β-units, the strands run parallel toeach other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641).The antisense nucleic acid molecule can also comprise a2′-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res.15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBSLett. 215:327-330).

In still another embodiment, an antisense nucleic acid of the inventionis a ribozyme. Ribozymes are catalytic RNA molecules with ribonucleaseactivity which are capable of cleaving a single-stranded nucleic acid,such as an mRNA, to which they have a complementary region. Thus,ribozymes (e.g., hammerhead ribozymes (described in Haselhoff andGerlach (1988) Nature 334:585-591)) can be used to catalytically cleaveSRT mRNA transcripts to thereby inhibit translation of SRT mRNA. Aribozyme having specificity for an SRT-encoding nucleic acid can bedesigned based upon the nucleotide sequence of an SRT cDNA disclosedherein (i.e., SEQ ID NO:119 (RXA00600 in Appendix A)). For example, aderivative of a Tetrahymena L-19 IVS RNA can be constructed in which thenucleotide sequence of the active site is complementary to thenucleotide sequence to be cleaved in an SRT-encoding mRNA. See, e.g.,Cech et al. U.S. Pat. No. 4,987,071 and Cech et al U.S. Pat. No.5,116,742. Alternatively, SRT mRNA can be used to select a catalytic RNAhaving a specific ribonuclease activity from a pool of RNA molecules.See, e.g., Bartel, D. and Szostak, J. W. (1993) Science 261:1411-1418.

Alternatively, SRT gene expression can be inhibited by targetingnucleotide sequences complementary to the regulatory region of an SRTnucleotide sequence (e.g., an SRT promoter and/or enhancers) to formtriple helical structures that prevent transcription of an SRT gene intarget cells. See generally, Helene, C. (1991) Anticancer Drug Des.6(6):569-84; Helene, C. et al. (1992) Ann. N.Y. Acad. Sci. 660:27-36;and Maher, L. J. (1992) Bioassays 14(12):807-15.

B. Recombinant Expression Vectors and Host Cells

Another aspect of the invention pertains to vectors, preferablyexpression vectors, containing a nucleic acid encoding an SRT protein(or a portion thereof). As used herein, the term “vector” refers to anucleic acid molecule capable of transporting another nucleic acid towhich it has been linked. One type of vector is a “plasmid”, whichrefers to a circular double stranded DNA loop into which additional DNAsegments can be ligated. Another type of vector is a viral vector,wherein additional DNA segments can be ligated into the viral genome.Certain vectors are capable of autonomous replication in a host cellinto which they are introduced (e.g., bacterial vectors having abacterial origin of replication and episomal mammalian vectors). Othervectors (e.g., non-episomal mammalian vectors) are integrated into thegenome of a host cell upon introduction into the host cell, and therebyare replicated along with the host genome. Moreover, certain vectors arecapable of directing the expression of genes to which they areoperatively linked. Such vectors are referred to herein as “expressionvectors”. In general, expression vectors of utility in recombinant DNAtechniques are often in the form of plasmids. In the presentspecification, “plasmid” and “vector” can be used interchangeably as theplasmid is the most commonly used form of vector. However, the inventionis intended to include such other forms of expression vectors, such asviral vectors (e.g., replication defective retroviruses, adenovirusesand adeno-associated viruses), which serve equivalent functions.

The recombinant expression vectors of the invention comprise a nucleicacid of the invention in a form suitable for expression of the nucleicacid in a host cell, which means that the recombinant expression vectorsinclude one or more regulatory sequences, selected on the basis of thehost cells to be used for expression, which is operatively linked to thenucleic acid sequence to be expressed. Within a recombinant expressionvector, “operably linked” is intended to mean that the nucleotidesequence of interest is linked to the regulatory sequence(s) in a mannerwhich allows for expression of the nucleotide sequence (e.g., in an invitro transcription/translation system or in a host cell when the vectoris introduced into the host cell). The term “regulatory sequence” isintended to include promoters, enhancers and other expression controlelements (e.g., polyadenylation signals). Such regulatory sequences aredescribed, for example, in Goeddel; Gene Expression Technology: Methodsin Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatorysequences include those which direct constitutive expression of anucleotide sequence in many types of host cell and those which directexpression of the nucleotide sequence only in certain host cells.Preferred regulatory sequences are, for example, promoters such as cos-,tac-, trp-, tet-, trp-tet-, lpp-, lac-, lpp-lac-, lacI^(q), T7-, T5-,T3-, gal-, trc-, ara-, SP6-, arny, SPO₂, λ-P_(R)- or λP_(L), which areused preferably in bacteria. Additional regulatory sequences are, forexample, promoters from yeasts and fungi, such as ADC1, MFα, AC, P-60,CYC1, GAPDH, TEF, rp28, ADH, promoters from plants such as CaMV/35S,SSU, OCS, lib4, usp, STLS1, B33, nos or ubiquitin- orphaseolin-promoters. It is also possible to use artificial promoters. Itwill be appreciated by one of ordinary skill in the art that the designof the expression vector can depend on such factors as the choice of thehost cell to be transformed, the level of expression of protein desired,etc. The expression vectors of the invention can be introduced into hostcells to thereby produce proteins or peptides, including fusion proteinsor peptides, encoded by nucleic acids as described herein (e.g., SRTproteins, mutant forms of SRT proteins, fusion proteins, etc.).

The recombinant expression vectors of the invention can be designed forexpression of SRT proteins in prokaryotic or eukaryotic cells. Forexample, SRT genes can be expressed in bacterial cells such as C.glutamicum, insect cells (using baculovirus expression vectors), yeastand other fungal cells (see Romanos, M. A. et al. (1992) “Foreign geneexpression in yeast: a review”, Yeast 8: 423-488; van den Hondel, C. A.M. J. J. et al. (1991) “Heterologous gene expression in filamentousfungi” in: More Gene Manipulations in Fungi, J. W. Bennet & L. L.Lasure, eds., p. 396-428: Academic Press: San Diego; and van den Hondel,C. A. M. J. J. & Punt, P. J. (1991) “Gene transfer systems and vectordevelopment for filamentous fungi, in: Applied Molecular Genetics ofFungi, Peberdy, J. F. et al., eds., p. 1-28, Cambridge University Press:Cambridge), algae and multicellular plant cells (see Schmidt, R. andWillmitzer, L. (1988) High efficiency Agrobacterium tumefaciens-mediatedtransformation of Arabidopsis thaliana leaf and cotyledon explants”Plant Cell Rep.: 583-586), or mammalian cells. Suitable host cells arediscussed further in Goeddel, Gene Expression Technology: Methods inEnzymology 185, Academic Press, San Diego, Calif. (1990). Alternatively,the recombinant expression vector can be transcribed and translated invitro, for example using T7 promoter regulatory sequences and T7polymerase.

Expression of proteins in prokaryotes is most often carried out withvectors containing constitutive or inducible promoters directing theexpression of either fusion or non-fusion proteins. Fusion vectors add anumber of amino acids to a protein encoded therein, usually to the aminoterminus of the recombinant protein. Such fusion vectors typically servethree purposes: 1) to increase expression of recombinant protein; 2) toincrease the solubility of the recombinant protein; and 3) to aid in thepurification of the recombinant protein by acting as a ligand inaffinity purification. Often, in fusion expression vectors, aproteolytic cleavage site is introduced at the junction of the fusionmoiety and the recombinant protein to enable separation of therecombinant protein from the fusion moiety subsequent to purification ofthe fusion protein. Such enzymes, and their cognate recognitionsequences, include Factor Xa, thrombin and enterokinase.

Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc;Smith, D. B. and Johnson, K. S. (1988) Gene 67:31-40), pMAL (New EnglandBiolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) whichfuse glutathione S-transferase (GST), maltose E binding protein, orprotein A, respectively, to the target recombinant protein. In oneembodiment, the coding sequence of the SRT protein is cloned into a pGEXexpression vector to create a vector encoding a fusion proteincomprising, from the N-terminus to the C-terminus, GST-thrombin cleavagesite-X protein. The fusion protein can be purified by affinitychromatography using glutathione-agarose resin. Recombinant SRT proteinunfused to GST can be recovered by cleavage of the fusion protein withthrombin.

Examples of suitable inducible non-fusion E. coli expression vectorsinclude pTrc (Amann et al., (1988) Gene 69:301-315) pLG338, pACYC184,pBR322, pUC18, pUC19, pKC30, pRep4, pHS1, pHS2, pPLc236, pMBL24, pLG200,pUR290, pIN-III113-B1, λgt11, pBdCl, and pET 11d (Studier et al., GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990) 60-89; and Pouwels et al., eds. (1985) CloningVectors. Elsevier: New York IBSN 0 444 904018). Target gene expressionfrom the pTrc vector relies on host RNA polymerase transcription from ahybrid trp-lac fusion promoter. Target gene expression from the pET 11dvector relies on transcription from a T7 gn10-lac fusion promotermediated by a coexpressed viral RNA polymerase (T7 gn1). This viralpolymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from aresident λ prophage harboring a T7 gn1 gene under the transcriptionalcontrol of the lacUV 5 promoter. For transformation of other varietiesof bacteria, appropriate vectors may be selected. For example, theplasmids pIJ101, pIJ364, pIJ702 and pIJ361 are known to be useful intransforming Streptomyces, while plasmids pUB110, pC194, or pBD214 aresuited for transformation of Bacillus species. Several plasmids of usein the transfer of genetic information into Corynebacterium includepHM1519, pBL1, pSA77, or pAJ667 (Pouwels et al., eds. (1985) CloningVectors. Elsevier: New York IBSN 0 444 904018).

One strategy to maximize recombinant protein expression is to expressthe protein in a host bacteria with an impaired capacity toproteolytically cleave the recombinant protein (Gottesman, S., GeneExpression Technology: Methods in Enzymology 185, Academic Press, SanDiego, Calif. (1990) 119-128). Another strategy is to alter the nucleicacid sequence of the nucleic acid to be inserted into an expressionvector so that the individual codons for each amino acid are thosepreferentially utilized in the bacterium chosen for expression, such asC. glutamicum (Wada et al. (1992) Nucleic Acids Res. 20:2111-2118). Suchalteration of nucleic acid sequences of the invention can be carried outby standard DNA synthesis techniques.

In another embodiment, the SRT protein expression vector is a yeastexpression vector. Examples of vectors for expression in yeast S.cerevisiae include pYepSec1 (Baldari, et al., (1987) Embo J. 6:229-234),2μ, pAG-1, Yep6, Yep13, pEMBLYe23, pMFa (Kurjan and Herskowitz, (1982)Cell 30:933-943), pJRY88 (Schultz et al., (1987) Gene 54:113-123), andpYES2 (Invitrogen Corporation, San Diego, Calif.). Vectors and methodsfor the construction of vectors appropriate for use in other fungi, suchas the filamentous fungi, include those detailed in: van den Hondel, C.A. M. J. J. & Punt, P. J. (1991) “Gene transfer systems and vectordevelopment for filamentous fungi, in: Applied Molecular Genetics ofFungi, J. F. Peberdy, et al., eds., p. 1-28, Cambridge University Press:Cambridge, and Pouwels et al., eds. (1985) Cloning Vectors. Elsevier:New York (IBSN 0 444 904018).

Alternatively, the SRT proteins of the invention can be expressed ininsect cells using baculovirus expression vectors. Baculovirus vectorsavailable for expression of proteins in cultured insect cells (e.g., Sf9cells) include the pAc series (Smith et al. (1983) Mol. Cell Biol.3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology170:31-39).

In another embodiment, the SRT proteins of the invention may beexpressed in unicellular plant cells (such as algae) or in plant cellsfrom higher plants (e.g., the spermatophytes, such as crop plants).Examples of plant expression vectors include those detailed in: Becker,D., Kemper, E., Schell, J. and Masterson, R. (1992) “New plant binaryvectors with selectable markers located proximal to the left border”,Plant Mol. Biol. 20: 1195-1197; and Bevan, M. W. (1984) “BinaryAgrobacterium vectors for plant transformation”, Nucl. Acid. Res. 12:8711-8721, and include pLGV23, pGHlac+, pBIN19, pAK2004, and pDH51(Pouwels et al., eds. (1985) Cloning Vectors. Elsevier: New York IBSN 0444 904018).

In yet another embodiment, a nucleic acid of the invention is expressedin mammalian cells using a mammalian expression vector. Examples ofmammalian expression vectors include pCDM8 (Seed, B. (1987) Nature329:840) and pMT2PC (Kaufman et al. (1987) EMBO J. 6:187-195). When usedin mammalian cells, the expression vector's control functions are oftenprovided by viral regulatory elements. For example, commonly usedpromoters are derived from polyoma, Adenovirus 2, cytomegalovirus andSimian Virus 40. For other suitable expression systems for bothprokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J.,Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual.2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., 1989.

In another embodiment, the recombinant mammalian expression vector iscapable of directing expression of the nucleic acid preferentially in aparticular cell type (e.g., tissue-specific regulatory elements are usedto express the nucleic acid). Tissue-specific regulatory elements areknown in the art. Non-limiting examples of suitable tissue-specificpromoters include the albumin promoter (liver-specific; Pinkert et al.(1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame andEaton (1988) Adv. Immunol. 43:235-275), in particular promoters of Tcell receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) andimmunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen andBaltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g., theneurofilament promoter; Byrne and Ruddle (1989) PNAS 86:5473-5477),pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916),and mammary gland-specific promoters (e.g., milk whey promoter; U.S.Pat. No. 4,873,316 and European Application Publication No. 264,166).Developmentally-regulated promoters are also encompassed, for examplethe murine hox promoters (Kessel and Gruss (1990) Science 249:374-379)and the α-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev.3:537-546).

The invention further provides a recombinant expression vectorcomprising a DNA molecule of the invention cloned into the expressionvector in an antisense orientation. That is, the DNA molecule isoperatively linked to a regulatory sequence in a manner which allows forexpression (by transcription of the DNA molecule) of an RNA moleculewhich is antisense to SRT mRNA. Regulatory sequences operatively linkedto a nucleic acid cloned in the antisense orientation can be chosenwhich direct the continuous expression of the antisense RNA molecule ina variety of cell types, for instance viral promoters and/or enhancers,or regulatory sequences can be chosen which direct constitutive, tissuespecific or cell type specific expression of antisense RNA. Theantisense expression vector can be in the form of a recombinant plasmid,phagemid or attenuated virus in which antisense nucleic acids areproduced under the control of a high efficiency regulatory region, theactivity of which can be determined by the cell type into which thevector is introduced. For a discussion of the regulation of geneexpression using antisense genes see Weintraub, H. et al., Antisense RNAas a molecular tool for genetic analysis, Reviews—Trends in Genetics,Vol. 1(1) 1986.

Another aspect of the invention pertains to host cells into which arecombinant expression vector of the invention has been introduced. Theterms “host cell” and “recombinant host cell” are used interchangeablyherein. It is understood that such terms refer not only to theparticular subject cell but to the progeny or potential progeny of sucha cell. Because certain modifications may occur in succeedinggenerations due to either mutation or environmental influences, suchprogeny may not, in fact, be identical to the parent cell, but are stillincluded within the scope of the term as used herein.

A host cell can be any prokaryotic or eukaryotic cell. For example, anSRT protein can be expressed in bacterial cells such as C. glutamicum,insect cells, yeast or mammalian cells (such as Chinese hamster ovarycells (CHO) or COS cells). Other suitable host cells are known to thoseof ordinary skill in the art. Microorganisms related to Corynebacteriumglutamicum which may be conveniently used as host cells for the nucleicacid and protein molecules of the invention are set forth in Table 3.

Vector DNA can be introduced into prokaryotic or eukaryotic cells viaconventional transformation or transfection techniques. As used herein,the terms “transformation” and “transfection” are intended to refer to avariety of art-recognized techniques for introducing foreign nucleicacid (e.g., linear DNA or RNA (e.g., a linearized vector or a geneconstruct alone without a vector) or nucleic acid in the form of avector (e.g., a plasmid, phage, phasmid, phagemid, transposon or otherDNA)) into a host cell, including calcium phosphate or calcium chlorideco-precipitation, DEAE-dextran-mediated transfection, lipofection, orelectroporation. Suitable methods for transforming or transfecting hostcells can be found in Sambrook, et al. (Molecular Cloning: A LaboratoryManual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1989), and other laboratorymanuals.

For stable transfection of mammalian cells, it is known that, dependingupon the expression vector and transfection technique used, only a smallfraction of cells may integrate the foreign DNA into their genome. Inorder to identify and select these integrants, a gene that encodes aselectable marker (e.g., resistance to antibiotics) is generallyintroduced into the host cells along with the gene of interest.Preferred selectable markers include those which confer resistance todrugs, such as G418, hygromycin and methotrexate. Nucleic acid encodinga selectable marker can be introduced into a host cell on the samevector as that encoding an SRT protein or can be introduced on aseparate vector. Cells stably transfected with the introduced nucleicacid can be identified by drug selection (e.g., cells that haveincorporated the selectable marker gene will survive, while the othercells die).

To create a homologous recombinant microorganism, a vector is preparedwhich contains at least a portion of an SRT gene into which a deletion,addition or substitution has been introduced to thereby alter, e.g.,functionally disrupt, the SRT gene. Preferably, this SRT gene is aCorynebacterium glutamicum SRT gene, but it can be a homologue from arelated bacterium or even from a mammalian, yeast, or insect source. Ina preferred embodiment, the vector is designed such that, uponhomologous recombination, the endogenous SRT gene is functionallydisrupted (i.e., no longer encodes a functional protein; also referredto as a “knock out” vector). Alternatively, the vector can be designedsuch that, upon homologous recombination, the endogenous SRT gene ismutated or otherwise altered but still encodes functional protein (e.g.,the upstream regulatory region can be altered to thereby alter theexpression of the endogenous SRT protein). In the homologousrecombination vector, the altered portion of the SRT gene is flanked atits 5′ and 3′ ends by additional nucleic acid of the SRT gene to allowfor homologous recombination to occur between the exogenous SRT genecarried by the vector and an endogenous SRT gene in a microorganism. Theadditional flanking SRT nucleic acid is of sufficient length forsuccessful homologous recombination with the endogenous gene. Typically,several kilobases of flanking DNA (both at the 5′ and 3′ ends) areincluded in the vector (see e.g., Thomas, K. R., and Capecchi, M. R.(1987) Cell 51: 503 for a description of homologous recombinationvectors). The vector is introduced into a microorganism (e.g., byelectroporation) and cells in which the introduced SRT gene hashomologously recombined with the endogenous SRT gene are selected, usingart-known techniques.

In another embodiment, recombinant microorganisms can be produced whichcontain selected systems which allow for regulated expression of theintroduced gene. For example, inclusion of an SRT gene on a vectorplacing it under control of the lac operon permits expression of the SRTgene only in the presence of IPTG. Such regulatory systems are wellknown in the art.

In another embodiment, an endogenous SRT gene in a host cell isdisrupted (e.g., by homologous recombination or other genetic meansknown in the art) such that expression of its protein product does notoccur. In another embodiment, an endogenous or introduced SRT gene in ahost cell has been altered by one or more point mutations, deletions, orinversions, but still encodes a functional SRT protein. In still anotherembodiment, one or more of the regulatory regions (e.g., a promoter,repressor, or inducer) of an SRT gene in a microorganism has beenaltered (e.g., by deletion, truncation, inversion, or point mutation)such that the expression of the SRT gene is modulated. One of ordinaryskill in the art will appreciate that host cells containing more thanone of the described SRT gene and protein modifications may be readilyproduced using the methods of the invention, and are meant to beincluded in the present invention.

A host cell of the invention, such as a prokaryotic or eukaryotic hostcell in culture, can be used to produce (i.e., express) an SRT protein.Accordingly, the invention further provides methods for producing SRTproteins using the host cells of the invention. In one embodiment, themethod comprises culturing the host cell of invention (into which arecombinant expression vector encoding an SRT protein has beenintroduced, or into which genome has been introduced a gene encoding awild-type or altered SRT protein) in a suitable medium until SRT proteinis produced. In another embodiment, the method further comprisesisolating SRT proteins from the medium or the host cell.

C. Isolated SRT Proteins

Another aspect of the invention pertains to isolated SRT proteins, andbiologically active portions thereof. An “isolated” or “purified”protein or biologically active portion thereof is substantially free ofcellular material when produced by recombinant DNA techniques, orchemical precursors or other chemicals when chemically synthesized. Thelanguage “substantially free of cellular material” includes preparationsof SRT protein in which the protein is separated from cellularcomponents of the cells in which it is naturally or recombinantlyproduced. In one embodiment, the language “substantially free ofcellular material” includes preparations of SRT protein having less thanabout 30% (by dry weight) of non-SRT protein (also referred to herein asa “contaminating protein”), more preferably less than about 20% ofnon-SRT protein, still more preferably less than about 10% of non-SRTprotein, and most preferably less than about 5% non-SRT protein. Whenthe SRT protein or biologically active portion thereof is recombinantlyproduced, it is also preferably substantially free of culture medium,i.e., culture medium represents less than about 20%, more preferablyless than about 10%, and most preferably less than about 5% of thevolume of the protein preparation. The language “substantially free ofchemical precursors or other chemicals” includes preparations of SRTprotein in which the protein is separated from chemical precursors orother chemicals which are involved in the synthesis of the protein. Inone embodiment, the language “substantially free of chemical precursorsor other chemicals” includes preparations of SRT protein having lessthan about 30% (by dry weight) of chemical precursors or non-SRTchemicals, more preferably less than about 20% chemical precursors ornon-SRT chemicals, still more preferably less than about 10% chemicalprecursors or non-SRT chemicals, and most preferably less than about 5%chemical precursors or non-SRT chemicals. In preferred embodiments,isolated proteins or biologically active portions thereof lackcontaminating proteins from the same organism from which the SRT proteinis derived. Typically, such proteins are produced by recombinantexpression of, for example, a C. glutamicum SRT protein in amicroorganism such as C. glutamicum.

An isolated SRT protein or a portion thereof of the invention cancontribute to the resistance or tolerance of C. glutamicum to one ormore chemical or environmental stresses or hazards, or has one or moreof the activities set forth in Table 1. In preferred embodiments, theprotein or portion thereof comprises an amino acid sequence which issufficiently homologous to an amino acid sequence of Appendix B suchthat the protein or portion thereof maintains the ability to mediate theresistance or tolerance of C. glutamicum to one or more chemical orenvironmental stresses or hazards. The portion of the protein ispreferably a biologically active portion as described herein. In anotherpreferred embodiment, an SRT protein of the invention has an amino acidsequence shown in Appendix B. In yet another preferred embodiment, theSRT protein has an amino acid sequence which is encoded by a nucleotidesequence which hybridizes, e.g., hybridizes under stringent conditions,to a nucleotide sequence of Appendix A. In still another preferredembodiment, the SRT protein has an amino acid sequence which is encodedby a nucleotide sequence that is at least about 50%, 51%, 52%, 53%, 54%,55%, 56%, 57%, 58%, 59%, or 60%, preferably at least about 61%, 62%,63%, 64%, 65%, 66%, 67%, 68%, 69%, or 70%, more preferably at leastabout 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, or 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, or 90%, or 91%, 92%, 93%, 94%, andeven more preferably at least about 95%, 96%, 97%, 98%, 99% or morehomologous to one of the nucleic acid sequences of Appendix A, or aportion thereof. Ranges and identity values intermediate to theabove-recited values, (e.g., 70-90% identical or 80-95% identical) arealso intended to be encompassed by the present invention. For example,ranges of identity values using a combination of any of the above valuesrecited as upper and/or lower limits are intended to be included. Thepreferred SRT proteins of the present invention also preferably possessat least one of the SRT activities described herein. For example, apreferred SRT protein of the present invention includes an amino acidsequence encoded by a nucleotide sequence which hybridizes, e.g.,hybridizes under stringent conditions, to a nucleotide sequence ofAppendix A, and which can increase the resistance or tolerance of C.glutamicum to one or more environmental or chemical stresses, or whichhas one or more of the activities set forth in Table 1.

In other embodiments, the SRT protein is substantially homologous to anamino acid sequence of Appendix B and retains the functional activity ofthe protein of one of the sequences of Appendix B yet differs in aminoacid sequence due to natural variation or mutagenesis, as described indetail in subsection I above. Accordingly, in another embodiment, theSRT protein is a protein which comprises an amino acid sequence which isat least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, or 60%,preferably at least about 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%,or 70%, more preferably at least about 71%, 72%, 73%, 74%, 75%, 76%,77%, 78%, 79%, or 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, or90%, or 91%, 92%, 93%, 94%, and even more preferably at least about 95%,96%, 97%, 98%, 99% or more homologous to an entire amino acid sequenceof Appendix B and which has at least one of the SRT activities describedherein. Ranges and identity values intermediate to the above-recitedvalues, (e.g., 70-90% identical or 80-95% identical) are also intendedto be encompassed by the present invention. For example, ranges ofidentity values using a combination of any of the above values recitedas upper and/or lower limits are intended to be included. In anotherembodiment, the invention pertains to a full length C. glutamicumprotein which is substantially homologous to an entire amino acidsequence of Appendix B.

Biologically active portions of an SRT protein include peptidescomprising amino acid sequences derived from the amino acid sequence ofan SRT protein, e.g., an amino acid sequence shown in Appendix B or theamino acid sequence of a protein homologous to an SRT protein, whichinclude fewer amino acids than a full length SRT protein or the fulllength protein which is homologous to an SRT protein, and exhibit atleast one activity of an SRT protein. Typically, biologically activeportions (peptides, e.g., peptides which are, for example, 5, 10, 15,20, 30, 35, 36, 37, 38, 39, 40, 50, 100 or more amino acids in length)comprise a domain or motif with at least one activity of an SRT protein.Moreover, other biologically active portions, in which other regions ofthe protein are deleted, can be prepared by recombinant techniques andevaluated for one or more of the activities described herein.Preferably, the biologically active portions of an SRT protein includeone or more selected domains/motifs or portions thereof havingbiological activity.

SRT proteins are preferably produced by recombinant DNA techniques. Forexample, a nucleic acid molecule encoding the protein is cloned into anexpression vector (as described above), the expression vector isintroduced into a host cell (as described above) and the SRT protein isexpressed in the host cell. The SRT protein can then be isolated fromthe cells by an appropriate purification scheme using standard proteinpurification techniques. Alternative to recombinant expression, an SRTprotein, polypeptide, or peptide can be synthesized chemically usingstandard peptide synthesis techniques. Moreover, native SRT protein canbe isolated from cells (e.g., endothelial cells), for example using ananti-SRT antibody, which can be produced by standard techniquesutilizing an SRT protein or fragment thereof of this invention.

The invention also provides SRT chimeric or fusion proteins. As usedherein, an SRT “chimeric protein” or “fusion protein” comprises an SRTpolypeptide operatively linked to a non-SRT polypeptide. An “SRTpolypeptide” refers to a polypeptide having an amino acid sequencecorresponding to SRT, whereas a “non-SRT polypeptide” refers to apolypeptide having an amino acid sequence corresponding to a proteinwhich is not substantially homologous to the SRT protein, e.g., aprotein which is different from the SRT protein and which is derivedfrom the same or a different organism. Within the fusion protein, theterm “operatively linked” is intended to indicate that the SRTpolypeptide and the non-SRT polypeptide are fused in-frame to eachother. The non-SRT polypeptide can be fused to the N-terminus orC-terminus of the SRT polypeptide. For example, in one embodiment thefusion protein is a GST-SRT fusion protein in which the SRT sequencesare fused to the C-terminus of the GST sequences. Such fusion proteinscan facilitate the purification of recombinant SRT proteins. In anotherembodiment, the fusion protein is an SRT protein containing aheterologous signal sequence at its N-terminus. In certain host cells(e.g., mammalian host cells), expression and/or secretion of an SRTprotein can be increased through use of a heterologous signal sequence.

Preferably, an SRT chimeric or fusion protein of the invention isproduced by standard recombinant DNA techniques. For example, DNAfragments coding for the different polypeptide sequences are ligatedtogether in-frame in accordance with conventional techniques, forexample by employing blunt-ended or stagger-ended termini for ligation,restriction enzyme digestion to provide for appropriate termini,filling-in of cohesive ends as appropriate, alkaline phosphatasetreatment to avoid undesirable joining, and enzymatic ligation. Inanother embodiment, the fusion gene can be synthesized by conventionaltechniques including automated DNA synthesizers. Alternatively, PCRamplification of gene fragments can be carried out using anchor primerswhich give rise to complementary overhangs between two consecutive genefragments which can subsequently be annealed and reamplified to generatea chimeric gene sequence (see, for example, Current Protocols inMolecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992).Moreover, many expression vectors are commercially available thatalready encode a fusion moiety (e.g., a GST polypeptide). AnSRT-encoding nucleic acid can be cloned into such an expression vectorsuch that the fusion moiety is linked in-frame to the SRT protein.

Homologues of the SRT protein can be generated by mutagenesis, e.g.,discrete point mutation or truncation of the SRT protein. As usedherein, the term “homologue” refers to a variant form of the SRT proteinwhich acts as an agonist or antagonist of the activity of the SRTprotein. An agonist of the SRT protein can retain substantially thesame, or a subset, of the biological activities of the SRT protein. Anantagonist of the SRT protein can inhibit one or more of the activitiesof the naturally occurring form of the SRT protein, by, for example,competitively binding to a downstream or upstream member of the SRTsystem which includes the SRT protein. Thus, the C. glutamicum SRTprotein and homologues thereof of the present invention may increase thetolerance or resistance of C. glutamicum to one or more chemical orenvironmental stresses.

In an alternative embodiment, homologues of the SRT protein can beidentified by screening combinatorial libraries of mutants, e.g.,truncation mutants, of the SRT protein for SRT protein agonist orantagonist activity. In one embodiment, a variegated library of SRTvariants is generated by combinatorial mutagenesis at the nucleic acidlevel and is encoded by a variegated gene library. A variegated libraryof SRT variants can be produced by, for example, enzymatically ligatinga mixture of synthetic oligonucleotides into gene sequences such that adegenerate set of potential SRT sequences is expressible as individualpolypeptides, or alternatively, as a set of larger fusion proteins(e.g., for phage display) containing the set of SRT sequences therein.There are a variety of methods which can be used to produce libraries ofpotential SRT homologues from a degenerate oligonucleotide sequence.Chemical synthesis of a degenerate gene sequence can be performed in anautomatic DNA synthesizer, and the synthetic gene then ligated into anappropriate expression vector. Use of a degenerate set of genes allowsfor the provision, in one mixture, of all of the sequences encoding thedesired set of potential SRT sequences. Methods for synthesizingdegenerate oligonucleotides are known in the art (see, e.g., Narang, S.A. (1983) Tetrahedron 39:3; Itakura et al. (1984) Annu. Rev. Biochem.53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983)Nucleic Acid Res. 11:477.

In addition, libraries of fragments of the SRT protein coding can beused to generate a variegated population of SRT fragments for screeningand subsequent selection of homologues of an SRT protein. In oneembodiment, a library of coding sequence fragments can be generated bytreating a double stranded PCR fragment of an SRT coding sequence with anuclease under conditions wherein nicking occurs only about once permolecule, denaturing the double stranded DNA, renaturing the DNA to formdouble stranded DNA which can include sense/antisense pairs fromdifferent nicked products, removing single stranded portions fromreformed duplexes by treatment with S1 nuclease, and ligating theresulting fragment library into an expression vector. By this method, anexpression library can be derived which encodes N-terminal, C-terminaland internal fragments of various sizes of the SRT protein.

Several techniques are known in the art for screening gene products ofcombinatorial libraries made by point mutations or truncation, and forscreening cDNA libraries for gene products having a selected property.Such techniques are adaptable for rapid screening of the gene librariesgenerated by the combinatorial mutagenesis of SRT homologues. The mostwidely used techniques, which are amenable to high through-put analysis,for screening large gene libraries typically include cloning the genelibrary into replicable expression vectors, transforming appropriatecells with the resulting library of vectors, and expressing thecombinatorial genes under conditions in which detection of a desiredactivity facilitates isolation of the vector encoding the gene whoseproduct was detected. Recursive ensemble mutagenesis (REM), a newtechnique which enhances the frequency of functional mutants in thelibraries, can be used in combination with the screening assays toidentify SRT homologues (Arkin and Yourvan (1992) PNAS 89:7811-7815;Delgrave et al. (1993) Protein Engineering 6(3):327-331).

In another embodiment, cell based assays can be exploited to analyze avariegated SRT library, using methods well known in the art.

D. Uses and Methods of the Invention

The nucleic acid molecules, proteins, protein homologues, fusionproteins, primers, vectors, and host cells described herein can be usedin one or more of the following methods: identification of C. glutamicumand related organisms; mapping of genomes of organisms related to C.glutamicum; identification and localization of C. glutamicum sequencesof interest; evolutionary studies; determination of SRT protein regionsrequired for function; modulation of an SRT protein activity; modulationof the activity of an SRT pathway; and modulation of cellular productionof a desired compound, such as a fine chemical.

The SRT nucleic acid molecules of the invention have a variety of uses.First, they may be used to identify an organism as being Corynebacteriumglutamicum or a close relative thereof. Also, they may be used toidentify the presence of C. glutamicum or a relative thereof in a mixedpopulation of microorganisms. The invention provides the nucleic acidsequences of a number of C. glutamicum genes; by probing the extractedgenomic DNA of a culture of a unique or mixed population ofmicroorganisms under stringent conditions with a probe spanning a regionof a C. glutamicum gene which is unique to this organism, one canascertain whether this organism is present.

Although Corynebacterium glutamicum itself is nonpathogenic, it isrelated to pathogenic species, such as Corynebacterium diphtheriae.Corynebacterium diphtheriae is the causative agent of diphtheria, arapidly developing, acute, febrile infection which involves both localand systemic pathology. In this disease, a local lesion develops in theupper respiratory tract and involves necrotic injury to epithelialcells; the bacilli secrete toxin which is disseminated through thislesion to distal susceptible tissues of the body. Degenerative changesbrought about by the inhibition of protein synthesis in these tissues,which include heart, muscle, peripheral nerves, adrenals, kidneys, liverand spleen, result in the systemic pathology of the disease. Diphtheriacontinues to have high incidence in many parts of the world, includingAfrica, Asia, Eastern Europe and the independent states of the formerSoviet Union. An ongoing epidemic of diphtheria in the latter tworegions has resulted in at least 5,000 deaths since 1990.

In one embodiment, the invention provides a method of identifying thepresence or activity of Cornyebacterium diphtheriae in a subject. Thismethod includes detection of one or more of the nucleic acid or aminoacid sequences of the invention (e.g., the sequences set forth inAppendix A or Appendix B) in a subject, thereby detecting the presenceor activity of Corynebacterium diphtheriae in the subject. C. glutamicumand C. diphtheriae are related bacteria, and many of the nucleic acidand protein molecules in C. glutamicum are homologous to C. diphtheriaenucleic acid and protein molecules, and can therefore be used to detectC. diphtheriae in a subject.

The nucleic acid and protein molecules of the invention may also serveas markers for specific regions of the genome. This has utility not onlyin the mapping of the genome, but also for functional studies of C.glutamicum proteins. For example, to identify the region of the genometo which a particular C. glutamicum DNA-binding protein binds, the C.glutamicum genome could be digested, and the fragments incubated withthe DNA-binding protein. Those which bind the protein may beadditionally probed with the nucleic acid molecules of the invention,preferably with readily detectable labels; binding of such a nucleicacid molecule to the genome fragment enables the localization of thefragment to the genome map of C. glutamicum, and, when performedmultiple times with different enzymes, facilitates a rapid determinationof the nucleic acid sequence to which the protein binds. Further, thenucleic acid molecules of the invention may be sufficiently homologousto the sequences of related species such that these nucleic acidmolecules may serve as markers for the construction of a genomic map inrelated bacteria, such as Brevibacterium lactofermentum.

The SRT nucleic acid molecules of the invention are also useful forevolutionary and protein structural studies. The resistance processes inwhich the molecules of the invention participate are utilized by a widevariety of cells; by comparing the sequences of the nucleic acidmolecules of the present invention to those encoding similar enzymesfrom other organisms, the evolutionary relatedness of the organisms canbe assessed. Similarly, such a comparison permits an assessment of whichregions of the sequence are conserved and which are not, which may aidin determining those regions of the protein which are essential for thefunctioning of the enzyme. This type of determination is of value forprotein engineering studies and may give an indication of what theprotein can tolerate in terms of mutagenesis without losing function.

The genes of the invention, e.g., the gene encoding LMRB (SEQ ID NO:1)or other gene of the invention encoding a chemical or environmentalresistance or tolerance protein (e.g., resistance against one or moreantibiotics), may be used as genetic markers for the genetictransformation of (e.g., the transfer of additional genes into ordisruption of preexisting genes of) organisms such as C. glutamicum orother bacterial species. Use of these nucleic acid molecules permitsefficient selection of organisms which have incorporated a giventransgene cassette (e.g., a plasmid, phage, phasmid, phagemid,transposon, or other nucleic acid element), based on a trait whichpermits the survival of the organism in an otherwise hostile or toxicenvironment (e.g., in the presence of an antimicrobial compound). Byemploying one or more of the genes of the invention as genetic markers,the speed and ease with which organisms having desirable transformedtraits (e.g., modulated fine chemical production) are engineered andisolated are improved. While it is advantageous to use the genes of theinvention for selection of transformed C. glutamicum and relatedbacteria, it is possible, as described herein, to use homologs (e.g.,homologs from other organisms), allelic variants or fragments of thegene retaining desired activity. Furthermore, 5′ and 3′ regulatoryelements of the genes of the invention may be modified as describedherein (e.g., by nucleotide substitution, insertion, deletion, orreplacement with a more desirable genetic element) to modulate thetranscription of the gene. For example, an LMRB variant in which thenucleotide sequence in the region from −1 to −200 5′ to the start codonhas been altered to modulate (preferably increase) the transcriptionand/or translation of LMRB may be employed, as can constructs in which agene of the invention (e.g., the LMRB gene (SEQ ID NO:1)) isfunctionally coupled to one or more regulatory signals (e.g., inducer orrepressor binding sequences) which can be used for modulating geneexpression. Similarly, more than one copy of a gene (functional orinactivated) of the invention may be employed.

An additional application of the genes of the invention (e.g., the geneencoding LMRB (SEQ ID NO:1) or other drug- or antibiotic-resistancegene) is in the discovery of new antibiotics which are active againstCorynebacteria and/or other bacteria. For example, a gene of theinvention may be expressed (or overexpressed) in a suitable host togenerate an organism with increased resistance to one or more drugs orantibiotics (in the case of LMRB, lincosamides in particular, especiallylincomycin). This type of resistant host can subsequently be used toscreen for chemicals with bacteriostatic and/or bacteriocidal activity,such as novel antibiotic compounds. It is possible, in particular, touse the genes of the invention (e.g., the LMRB gene) to identify newantibiotics which are active against those microorganisms which arealready resistant to standard antibiotic compounds.

The invention provides methods for screening molecules which modulatethe activity of an SRT protein, either by interacting with the proteinitself or a substrate or binding partner of the SRT protein, or bymodulating the transcription or translation of a SRT nucleic acidmolecule of the invention. In such methods, a microorganism expressingone or more SRT proteins of the invention is contacted with one or moretest compounds, and the effect of each test compound on the activity orlevel of expression of the SRT protein is assessed.

Manipulation of the SRT nucleic acid molecules of the invention mayresult in the production of SRT proteins having functional differencesfrom the wild-type SRT proteins. These proteins may be improved inefficiency or activity, may be present in greater numbers in the cellthan is usual, or may be decreased in efficiency or activity. The goalof such manipulations is to increase the viability and activity of thecell when the cell is exposed to the environmental and chemical stressesand hazards which frequently accompany large-scale fermentative culture.Thus, by increasing the activity or copy number of aheat-shock-regulated protease, one may increase the ability of the cellto destroy incorrectly folded proteins, which may otherwise interferewith normal cellular functioning (for example, by continuing to bindsubstrates or cofactors although the protein lacks the activity to acton these molecules appropriately). The same is true for theoverexpression or optimization of activity of one or more chaperonemolecules induced by heat or cold shock. These proteins aid in thecorrect folding of nascent polypeptide chains, and thus their increasedactivity or presence should increase the percentage of correctly foldedproteins in the cell, which in turn should increase the overallmetabolic efficiency and viability of the cells in culture. Theoverexpression or optimization of the transporter molecules activated byosmotic shock should result in an increased ability on the part of thecell to maintain intracellular homeostasis, thereby increasing theviability of these cells in culture. Similarly, the overproduction orincrease in activity by mutagenesis of proteins involved in thedevelopment of cellular resistance to chemical stresses of various kinds(either by transport of the offending chemical out of the cell or bymodification of the chemical to a less hazardous substance) shouldincrease the fitness of the organism in the environment containing thehazardous substance (i.e., large-scale fermentative culture), andthereby may permit relatively larger numbers of cells to survive in sucha culture. The net effect of all of these mutagenesis strategies is toincrease the quantity of fine-chemical-producing compounds in theculture, thereby increasing the yield, production, and/or efficiency ofproduction of one or more desired fine chemicals from the culture.

This aforementioned list of mutagenesis strategies for SRT proteins toresult in increased yields of a desired compound is not meant to belimiting; variations on these mutagenesis strategies will be readilyapparent to one of ordinary skill in the art. By these mechanisms, thenucleic acid and protein molecules of the invention may be utilized togenerate C. glutamicum or related strains of bacteria expressing mutatedSRT nucleic acid and protein molecules such that the yield, production,and/or efficiency of production of a desired compound is improved. Thisdesired compound may be any natural product of C. glutamicum, whichincludes the final products of biosynthesis pathways and intermediatesof naturally-occurring metabolic pathways, as well as molecules which donot naturally occur in the metabolism of C. glutamicum, but which areproduced by a C. glutamicum strain of the invention.

This invention is further illustrated by the following examples whichshould not be construed as limiting. The contents of all references,patent applications, patents, published patent applications, Tables,Appendices, and the sequence listing cited throughout this applicationare hereby incorporated by reference.

EXEMPLIFICATION Example 1 Preparation of Total Genomic DNA ofCorynebacterium glutamicum ATCC 13032

A culture of Corynebacterium glutamicum (ATCC 13032) was grown overnightat 30° C. with vigorous shaking in BHI medium (Difco). The cells wereharvested by centrifugation, the supernatant was discarded and the cellswere resuspended in 5 ml buffer-I (5% of the original volume of theculture—all indicated volumes have been calculated for 100 ml of culturevolume). Composition of buffer-I: 140.34 g/l sucrose, 2.46 g/lMgSO₄×7H₂O, 10 ml/l KH₂PO₄ solution (100 g/l, adjusted to pH 6.7 withKOH), 50 ml/l M12 concentrate (10 g/l (NH₄)₂SO₄, 1 g/l NaCl, 2 g/lMgSO₄×7H₂O, 0.2 g/l CaCl₂, 0.5 g/l yeast extract (Difco), 10 ml/ltrace-elements-mix (200 mg/l FeSO₄×H₂O, 10 mg/l ZnSO₄×7H₂O, 3 mg/lMnCl₂×4H₂O, 30 mg/l H₃BO₃ 20 mg/l CoCl₂×6H₂O, 1 mg/l NiCl₂×6H₂O, 3 mg/lNa₂MoO₄×2H₂O, 500 mg/l complexing agent (EDTA or critic acid), 100 ml/lvitamins-mix (0.2 mg/l biotin, 0.2 mg/l folic acid, 20 mg/l p-aminobenzoic acid, 20 mg/l riboflavin, 40 mg/l ca-panthothenate, 140 mg/lnicotinic acid, 40 mg/l pyridoxole hydrochloride, 200 mg/lmyo-inositol). Lysozyme was added to the suspension to a finalconcentration of 2.5 mg/ml. After an approximately 4 h incubation at 37°C., the cell wall was degraded and the resulting protoplasts areharvested by centrifugation. The pellet was washed once with 5 mlbuffer-I and once with 5 ml TE-buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8).The pellet was resuspended in 4 ml TE-buffer and 0.5 ml SDS solution(10%) and 0.5 ml NaCl solution (5 M) are added. After adding ofproteinase K to a final concentration of 200 μg/ml, the suspension isincubated for ca. 18 h at 37° C. The DNA was purified by extraction withphenol, phenol-chloroform-isoamylalcohol and chloroform-isoamylalcoholusing standard procedures. Then, the DNA was precipitated by adding 1/50volume of 3 M sodium acetate and 2 volumes of ethanol, followed by a 30min incubation at −20° C. and a 30 min centrifugation at 12,000 rpm in ahigh speed centrifuge using a SS34 rotor (Sorvall). The DNA wasdissolved in 1 ml TE-buffer containing 20 μg/ml RNaseA and dialysed at4° C. against 1000 ml TE-buffer for at least 3 hours. During this time,the buffer was exchanged 3 times. To aliquots of 0.4 ml of the dialysedDNA solution, 0.4 ml of 2 M LiCl and 0.8 ml of ethanol are added. Aftera 30 min incubation at −20° C., the DNA was collected by centrifugation(13,000 rpm, Biofuge Fresco, Heraeus, Hanau, Germany). The DNA pelletwas dissolved in TE-buffer. DNA prepared by this procedure could be usedfor all purposes, including southern blotting or construction of genomiclibraries.

Example 2 Construction of Genomic Libraries in Escherichia coli ofCorynebacterium glutamicum ATCC13032

Using DNA prepared as described in Example 1, cosmid and plasmidlibraries were constructed according to known and well establishedmethods (see e.g., Sambrook, J. et al. (1989) “Molecular Cloning: ALaboratory Manual”, Cold Spring Harbor Laboratory Press, or Ausubel, F.M. et al. (1994) “Current Protocols in Molecular Biology”, John Wiley &Sons.)

Any plasmid or cosmid could be used. Of particular use were the plasmidspBR322 (Sutcliffe, J. G. (1979) Proc. Natl. Acad. Sci. USA,75:3737-3741); pACYC177 (Change & Cohen (1978) J. Bacteriol134:1141-1156), plasmids of the pBS series (pBSSK+, pBSSK− and others;Stratagene, LaJolla, USA), or cosmids as SuperCos1 (Stratagene, LaJolla,USA) or Lorist6 (Gibson, T. J., Rosenthal A. and Waterson, R. H. (1987)Gene 53:283-286. Gene libraries specifically for use in C. glutamicummay be constructed using plasmid pSL109 (Lee, H.-S. and A. J. Sinskey(1994) J. Microbiol. Biotechnol. 4: 256-263).

Example 3 DNA Sequencing and Computational Functional Analysis

Genomic libraries as described in Example 2 were used for DNA sequencingaccording to standard methods, in particular by the chain terminationmethod using ABI377 sequencing machines (see e.g., Fleischman, R. D. etal. (1995) “Whole-genome Random Sequencing and Assembly of HaemophilusInfluenzae Rd., Science, 269:496-512). Sequencing primers with thefollowing nucleotide sequences were used: 5′-GGAAACAGTATGACCATG-3′ or5′-GTAAAACGACGGCCAGT-3′.

Example 4 In Vivo Mutagenesis

In vivo mutagenesis of Corynebacterium glutamicum can be performed bypassage of plasmid (or other vector) DNA through E. coli or othermicroorganisms (e.g. Bacillus spp. or yeasts such as Saccharomycescerevisiae) which are impaired in their capabilities to maintain theintegrity of their genetic information. Typical mutator strains havemutations in the genes for the DNA repair system (e.g., mutHLS, mutD,mutT, etc.; for reference, see Rupp, W. D. (1996) DNA repair mechanisms,in: Escherichia coli and Salmonella, p. 2277-2294, ASM: Washington.)Such strains are well known to those of ordinary skill in the art. Theuse of such strains is illustrated, for example, in Greener, A. andCallahan, M. (1994) Strategies _(—)7: 32-34.

Example 5 DNA Transfer Between Escherichia coli and Corynebacteriumglutamicum

Several Corynebacterium and Brevibacterium species contain endogenousplasmids (as e.g., pHM1519 or pBL1) which replicate autonomously (forreview see, e.g. Martin, J. F. et al. (1987) Biotechnology, 5:137-146).Shuttle vectors for Escherichia coli and Corynebacterium glutamicum canbe readily constructed by using standard vectors for E. coli (Sambrook,J. et al. (1989), “Molecular Cloning: A Laboratory Manual”, Cold SpringHarbor Laboratory Press or Ausubel, F. M. et al. (1994) “CurrentProtocols in Molecular Biology”, John Wiley & Sons) to which a origin orreplication for and a suitable marker from Corynebacterium glutamicum isadded. Such origins of replication are preferably taken from endogenousplasmids isolated from Corynebacterium and Brevibacterium species. Ofparticular use as transformation markers for these species are genes forkanamycin resistance (such as those derived from the Tn5 or Tn903transposons) or chloramphenicol (Winnacker, E. L. (1987) “From Genes toClones Introduction to Gene Technology, VCH, Weinheim). There arenumerous examples in the literature of the construction of a widevariety of shuttle vectors which replicate in both E. coli and C.glutamicum, and which can be used for several purposes, including geneover-expression (for reference, see e.g., Yoshihama, M. et al. (1985) J.Bacteriol. 162:591-597, Martin J. F. et al. (1987) Biotechnology,5:137-146 and Eikmanns, B. J. et al. (1991) Gene, 102:93-98).

Using standard methods, it is possible to clone a gene of interest intoone of the shuttle vectors described above and to introduce such ahybrid vector into strains of Corynebacterium glutamicum. Transformationof C. glutamicum can be achieved by protoplast transformation(Kastsumata, R. et al. (1984) J. Bacteriol. 159306-311), electroporation(Liebl, E. et al. (1989) FEMS Microbiol. Letters, 53:399-303) and incases where special vectors are used, also by conjugation (as describede.g. in Schafer, A et al. (1990) J. Bacteriol. 172:1663-1666). It isalso possible to transfer the shuttle vectors for C. glutamicum to E.coli by preparing plasmid DNA from C. glutamicum (using standard methodswell-known in the art) and transforming it into E. coli. Thistransformation step can be performed using standard methods, but it isadvantageous to use an Mcr-deficient E. coli strain, such as NM522(Gough & Murray (1983) J. Mol. Biol. 166:1-19).

Genes may be overexpressed in C. glutamicum strains using plasmids whichcomprise pCG1 (U.S. Pat. No. 4,617,267) or fragments thereof, andoptionally the gene for kanamycin resistance from TN903 (Grindley, N. D.and Joyce, C. M. (1980) Proc. Natl. Acad. Sci. USA 77(12): 7176-7180).In addition, genes may be overexpressed in C. glutamicum strains usingplasmid pSL109 (Lee, H.-S. and A. J. Sinskey (1994) J. Microbiol.Biotechnol. 4: 256-263).

Aside from the use of replicative plasmids, gene overexpression can alsobe achieved by integration into the genome. Genomic integration in C.glutamicum or other Corynebacterium or Brevibacterium species may beaccomplished by well-known methods, such as homologous recombinationwith genomic region(s), restriction endonuclease mediated integration(REMI) (see, e.g., DE Patent 19823834), or through the use oftransposons. It is also possible to modulate the activity of a gene ofinterest by modifying the regulatory regions (e.g., a promoter, arepressor, and/or an enhancer) by sequence modification, insertion, ordeletion using site-directed methods (such as homologous recombination)or methods based on random events (such as transposon mutagenesis orREMI). Nucleic acid sequences which function as transcriptionalterminators may also be inserted 3′ to the coding region of one or moregenes of the invention; such terminators are well-known in the art andare described, for example, in Winnacker, E. L. (1987) From Genes toClones—Introduction to Gene Technology. VCH: Weinheim.

Example 6 Assessment of the Expression of the Mutant Protein

Observations of the activity of a mutated protein in a transformed hostcell rely on the fact that the mutant protein is expressed in a similarfashion and in a similar quantity to that of the wild-type protein. Auseful method to ascertain the level of transcription of the mutant gene(an indicator of the amount of mRNA available for translation to thegene product) is to perform a Northern blot (for reference see, forexample, Ausubel et al. (1988) Current Protocols in Molecular Biology,Wiley: New York), in which a primer designed to bind to the gene ofinterest is labeled with a detectable tag (usually radioactive orchemiluminescent), such that when the total RNA of a culture of theorganism is extracted, run on gel, transferred to a stable matrix andincubated with this probe, the binding and quantity of binding of theprobe indicates the presence and also the quantity of mRNA for thisgene. This information is evidence of the degree of transcription of themutant gene. Total cellular RNA can be prepared from Corynebacteriumglutamicum by several methods, all well-known in the art, such as thatdescribed in Bormann, E. R. et al. (1992) Mol. Microbiol. 6: 317-326.

To assess the presence or relative quantity of protein translated fromthis mRNA, standard techniques, such as a Western blot, may be employed(see, for example, Ausubel et al. (1988) Current Protocols in MolecularBiology, Wiley: New York). In this process, total cellular proteins areextracted, separated by gel electrophoresis, transferred to a matrixsuch as nitrocellulose, and incubated with a probe, such as an antibody,which specifically binds to the desired protein. This probe is generallytagged with a chemiluminescent or calorimetric label which may bereadily detected. The presence and quantity of label observed indicatesthe presence and quantity of the desired mutant protein present in thecell.

Example 7 Growth of Genetically Modified Corynebacteriumglutamicum—Media and Culture Conditions

Genetically modified Corynebacteria are cultured in synthetic or naturalgrowth media. A number of different growth media for Corynebacteria areboth well-known and readily available (Lieb et al. (1989) Appl.Microbiol. Biotechnol., 32:205-210; von der Osten et al. (1998)Biotechnology Letters, 11:11-16; Patent DE 4,120,867; Liebl (1992) “TheGenus Corynebacterium, in: The Procaryotes, Volume II, Balows, A. etal., eds. Springer-Verlag). These media consist of one or more carbonsources, nitrogen sources, inorganic salts, vitamins and trace elements.Preferred carbon sources are sugars, such as mono-, di-, orpolysaccharides. For example, glucose, fructose, mannose, galactose,ribose, sorbose, ribulose, lactose, maltose, sucrose, raffinose, starchor cellulose serve as very good carbon sources. It is also possible tosupply sugar to the media via complex compounds such as molasses orother by-products from sugar refinement. It can also be advantageous tosupply mixtures of different carbon sources. Other possible carbonsources are alcohols and organic acids, such as methanol, ethanol,acetic acid or lactic acid. Nitrogen sources are usually organic orinorganic nitrogen compounds, or materials which contain thesecompounds. Exemplary nitrogen sources include ammonia gas or ammoniasalts, such as NH₄Cl or (NH₄)₂SO₄, NH₄OH, nitrates, urea, amino acids orcomplex nitrogen sources like corn steep liquor, soy bean flour, soybean protein, yeast extract, meat extract and others.

Inorganic salt compounds which may be included in the media include thechloride-, phosphorous- or sulfate-salts of calcium, magnesium, sodium,cobalt, molybdenum, potassium, manganese, zinc, copper and iron.Chelating compounds can be added to the medium to keep the metal ions insolution. Particularly useful chelating compounds includedihydroxyphenols, like catechol or protocatechuate, or organic acids,such as citric acid. It is typical for the media to also contain othergrowth factors, such as vitamins or growth promoters, examples of whichinclude biotin, riboflavin, thiamin, folic acid, nicotinic acid,pantothenate and pyridoxin. Growth factors and salts frequentlyoriginate from complex media components such as yeast extract, molasses,corn steep liquor and others. The exact composition of the mediacompounds depends strongly on the immediate experiment and isindividually decided for each specific case. Information about mediaoptimization is available in the textbook “Applied Microbiol.Physiology, A Practical Approach (eds. P. M. Rhodes, P. F. Stanbury, IRLPress (1997) pp. 53-73, ISBN 0 19 963577 3). It is also possible toselect growth media from commercial suppliers, like standard 1 (Merck)or BHI (grain heart infusion, DIFCO) or others.

All medium components are sterilized, either by heat (20 minutes at 1.5bar and 121° C.) or by sterile filtration. The components can either besterilized together or, if necessary, separately. All media componentscan be present at the beginning of growth, or they can optionally beadded continuously or batchwise.

Culture conditions are defined separately for each experiment. Thetemperature should be in a range between 15° C. and 45° C. Thetemperature can be kept constant or can be altered during theexperiment. The pH of the medium should be in the range of 5 to 8.5,preferably around 7.0, and can be maintained by the addition of buffersto the media. An exemplary buffer for this purpose is a potassiumphosphate buffer. Synthetic buffers such as MOPS, HEPES, ACES and otherscan alternatively or simultaneously be used. It is also possible tomaintain a constant culture pH through the addition of NaOH or NH₄OHduring growth. If complex medium components such as yeast extract areutilized, the necessity for additional buffers may be reduced, due tothe fact that many complex compounds have high buffer capacities. If afermentor is utilized for culturing the microorganisms, the pH can alsobe controlled using gaseous ammonia.

The incubation time is usually in a range from several hours to severaldays. This time is selected in order to permit the maximal amount ofproduct to accumulate in the broth. The disclosed growth experiments canbe carried out in a variety of vessels, such as microtiter plates, glasstubes, glass flasks or glass or metal fermentors of different sizes. Forscreening a large number of clones, the microorganisms should becultured in microtiter plates, glass tubes or shake flasks, either withor without baffles. Preferably 100 ml shake flasks are used, filled with10% (by volume) of the required growth medium. The flasks should beshaken on a rotary shaker (amplitude 25 mm) using a speed-range of100-300 rpm. Evaporation losses can be diminished by the maintenance ofa humid atmosphere; alternatively, a mathematical correction forevaporation losses should be performed.

If genetically modified clones are tested, an unmodified control cloneor a control clone containing the basic plasmid without any insertshould also be tested. The medium is inoculated to an OD₆₀₀ of 0.5-1.5using cells grown on agar plates, such as CM plates (10 g/l glucose, 2.5g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeast extract, 5 g/lmeat extract, 22 g/l NaCl, 2 g/l urea, 10 g/l polypeptone, 5 g/l yeastextract, 5 g/l meat extract, 22 g/l agar, pH 6.8 with 2M NaOH) that hadbeen incubated at 30° C. Inoculation of the media is accomplished byeither introduction of a saline suspension of C. glutamicum cells fromCM plates or addition of a liquid preculture of this bacterium.

Example 8 In Vitro Analysis of the Function of Mutant Proteins

The determination of activities and kinetic parameters of enzymes iswell established in the art. Experiments to determine the activity ofany given altered enzyme must be tailored to the specific activity ofthe wild-type enzyme, which is well within the ability of one ofordinary skill in the art. Overviews about enzymes in general, as wellas specific details concerning structure, kinetics, principles, methods,applications and examples for the determination of many enzymeactivities may be found, for example, in the following references:Dixon, M., and Webb, E. C., (1979) Enzymes. Longmans: London; Fersht,(1985) Enzyme Structure and Mechanism. Freeman: New York; Walsh, (1979)Enzymatic Reaction Mechanisms. Freeman: San Francisco; Price, N. C.,Stevens, L. (1982) Fundamentals of Enzymology. Oxford Univ. Press:Oxford; Boyer, P. D., ed. (1983) The Enzymes, 3^(rd) ed. Academic Press:New York; Bisswanger, H., (1994) Enzymkinetik, 2^(nd) ed. VCH: Weinheim(ISBN 3527300325); Bergmeyer, H. U., Bergmeyer, J., Graβ1, M., eds.(1983-1986) Methods of Enzymatic Analysis, 3^(rd) ed., vol. I-XII,Verlag Chemie: Weinheim; and Ullmann's Encyclopedia of IndustrialChemistry (1987) vol. A9, “Enzymes”. VCH: Weinheim, p. 352-363.

The activity of proteins which bind to DNA can be measured by severalwell-established methods, such as DNA band-shift assays (also called gelretardation assays). The effect of such proteins on the expression ofother molecules can be measured using reporter gene assays (such as thatdescribed in Kolmar, H. et al. (1995) EMBO J. 14: 3895-3904 andreferences cited therein). Reporter gene test systems are well known andestablished for applications in both pro- and eukaryotic cells, usingenzymes such as beta-galactosidase, green fluorescent protein, andseveral others.

The determination of activity of membrane-transport proteins can beperformed according to techniques such as those described in Gennis, R.B. (1989) “Pores, Channels and Transporters”, in Biomembranes, MolecularStructure and Function, Springer: Heidelberg, p. 85-137; 199-234; and270-322.

Example 9 Analysis of Impact of Mutant Protein on the Production of theDesired Product

The effect of the genetic modification in C. glutamicum on production ofa desired compound (such as an amino acid) can be assessed by growingthe modified microorganism under suitable conditions (such as thosedescribed above) and analyzing the medium and/or the cellular componentfor increased production of the desired product (i.e., an amino acid).Such analysis techniques are well known to one of ordinary skill in theart, and include spectroscopy, thin layer chromatography, stainingmethods of various kinds, enzymatic and microbiological methods, andanalytical chromatography such as high performance liquid chromatography(see, for example, Ullman, Encyclopedia of Industrial Chemistry, vol.A2, p. 89-90 and p. 443-613, VCH: Weinheim (1985); Fallon, A. et al.,(1987) “Applications of HPLC in Biochemistry” in: Laboratory Techniquesin Biochemistry and Molecular Biology, vol. 17; Rehm et al. (1993)Biotechnology, vol. 3, Chapter III: “Product recovery and purification”,page 469-714, VCH: Weinheim; Belter, P. A. et al. (1988) Bioseparations:downstream processing for biotechnology, John Wiley and Sons; Kennedy,J. F. and Cabral, J. M. S. (1992) Recovery processes for biologicalmaterials, John Wiley and Sons; Shaeiwitz, J. A. and Henry, J. D. (1988)Biochemical separations, in: Ulmann's Encyclopedia of IndustrialChemistry, vol. B3, Chapter 11, page 1-27, VCH: Weinheim; and Dechow, F.J. (1989) Separation and purification techniques in biotechnology, NoyesPublications.)

In addition to the measurement of the final product of fermentation, itis also possible to analyze other components of the metabolic pathwaysutilized for the production of the desired compound, such asintermediates and side-products, to determine the overall yield,production, and/or efficiency of production of the compound. Analysismethods include measurements of nutrient levels in the medium (e.g.,sugars, hydrocarbons, nitrogen sources, phosphate, and other ions),measurements of biomass composition and growth, analysis of theproduction of common metabolites of biosynthetic pathways, andmeasurement of gasses produced during fermentation. Standard methods forthese measurements are outlined in Applied Microbial Physiology, APractical Approach, P. M. Rhodes and P. F. Stanbury, eds., IRL Press, p.103-129; 131-163; and 165-192 (ISBN: 0199635773) and references citedtherein.

Example 10 Purification of the Desired Product from C. glutamicumCulture

Recovery of the desired product from the C. glutamicum cells orsupernatant of the above-described culture can be performed by variousmethods well known in the art. If the desired product is not secretedfrom the cells, the cells can be harvested from the culture by low-speedcentrifugation, the cells can be lysed by standard techniques, such asmechanical force or sonication. The cellular debris is removed bycentrifugation, and the supernatant fraction containing the solubleproteins is retained for further purification of the desired compound.If the product is secreted from the C. glutamicum cells, then the cellsare removed from the culture by low-speed centrifugation, and thesupernate fraction is retained for further purification.

The supernatant fraction from either purification method is subjected tochromatography with a suitable resin, in which the desired molecule iseither retained on a chromatography resin while many of the impuritiesin the sample are not, or where the impurities are retained by the resinwhile the sample is not. Such chromatography steps may be repeated asnecessary, using the same or different chromatography resins. One ofordinary skill in the art would be well-versed in the selection ofappropriate chromatography resins and in their most efficaciousapplication for a particular molecule to be purified. The purifiedproduct may be concentrated by filtration or ultrafiltration, and storedat a temperature at which the stability of the product is maximized.

There are a wide array of purification methods known to the art and thepreceding method of purification is not meant to be limiting. Suchpurification techniques are described, for example, in Bailey, J. E. &Ollis, D. F. Biochemical Engineering Fundamentals, McGraw-Hill: New York(1986).

The identity and purity of the isolated compounds may be assessed bytechniques standard in the art. These include high-performance liquidchromatography (HPLC), spectroscopic methods, staining methods, thinlayer chromatography, NIRS, enzymatic assay, or microbiologically. Suchanalysis methods are reviewed in: Patek et al. (1994) Appl. Environ.Microbiol. 60: 133-140; Malakhova et al. (1996) Biotekhnologiya 11:27-32; and Schmidt et al. (1998) Bioprocess Engineer. 19: 67-70.Ulmann's Encyclopedia of Industrial Chemistry, (1996) vol. A27, VCH:Weinheim, p. 89-90, p. 521-540, p. 540-547, p. 559-566, 575-581 and p.581-587; Michal, G. (1999) Biochemical Pathways: An Atlas ofBiochemistry and Molecular Biology, John Wiley and Sons; Fallon, A. etal. (1987) Applications of HPLC in Biochemistry in: LaboratoryTechniques in Biochemistry and Molecular Biology, vol. 17.

Example 11 Cloning of a Corynebacterium glutamicum Gene Involved inLincomycin Resistance Using a Reporter Gene Approach

A. Identification of the Gene Encoding the LMRB Protein

Plasmid pSL130 was constructed by ligation of the aceB promoter region(paceB) of C. glutamicum (Kim, H. J. et al. (1997) J. Microbiol.Biotechnol. 7: 287-292) into the polylinker of the lac operon fusionvector pRS415, which lacks a promoter (Simon, R. W. et al. (1987) Gene53: 85-96). Plasmid pSL145 was constructed by ligating the resultingpaceB-lac region into the E. coli cloning vector pACYC 184. E. coliDH5αF′ was transformed with pSL145 and the resulting strain was used asa host for screening of a genomic C. glutamicum library (in pSL109).

Transformants were screened by growth on agar medium containing5-bromo-4-chloro-3-indolyl-beta-D-glalactopyranoside (X-Gal). A whitecolony, containing DNA influencing lacZ expression, was selected forfurther analysis. This clone was found to contain a 4 kB fragment fromthe gene library. Subclones were constructed in pSL109 and a subclonewhich retained the white phenotype on X-Gal plates was identified. Thissubclone was found to contain a 2.6 kB BamH1-XhoI fragment (plasmidpSL149-5). The fragment was sequenced and identified as a membraneprotein-encoding gene (LMRB gene).

The 1442 nucleotides of the coding sequence of the LMRB gene encode apolypeptide of 481 amino acid residues with a high percentage ofhydrophobic amino acids. A Genbank search determined that the LMRBprotein is 40% identical to the protein product of the lmrB gene fromBacillus subtilis (Genbank Accession AL009126, TREMBL Accession P94422),as determined using a CLUSTAL W analysis (using standard parameters).

The LMRN protein contains a sequence pattern:158-A-P-A-L-G-P-T-L-S-G-167 (SEQ ID NO:301), which resembles the knownmulti-drug-resistance-protein consensus motif G-X-X-X-G-P-X-X-G-G (SEQID NO:302) (Paulsen, I. T., and Skurray, R. A. (1993) Gene 124: 1-11).Therefore, the LMRB protein was classified as a drug resistance protein.

B. In Vivo Analysis of lmrB Function

The lmrB gene was overexpressed in C. glutamicum ASO19E12 (Kim, H. J. etal. (1997) J. Microbiol. Biotechnol. 7: 287-292) using the plasmidpSL149-5, described above.

Disruption of the LMRB gene was accomplished by use of the vectorpSL18-lmrB. This vector was constructed as follows: an internal fragmentof the LMRB gene was amplified by PCR under standard conditions usingprimers 5′-CTCCAGGATTGCTCCGAAGG-3′ (SEQ ID NO:303) and5′-CACAGTGGTTGACCACTGGC-3′ (SEQ ID NO:304). The resulting PCR productwas treated with T7 DNA polymerase and T7 polynucleotide kinase, and wascloned into the SmaI site of plasmid pSL18 (Kim, Y. H. and H.-S. Lee(1996) J. Microbiol. Biotechnol. 6: 315-320). The disruption of the LMRBgene in C. glutamicum ASO19E12 was performed by conjugation, aspreviously described (Schwarzer and Puhler (1991) Bio/Technology9:84-87).

C. glutamicum cells transformed with pSL149-5 displayed similarresistances as untransformed cells against erythromycin, penicillin G,tetracycline, chloramphenicol, spectinomycin, nalidixic acid,gentamycin, streptomycin, ethidium bromide, carbonyl cyanidem-chlorophenylhydrazone (CCCP), and sodium dodecyl sulfate. Significantdifferences were observed, however, in the resistance of transformed anduntransformed cells to lincomycin.

LMRB-overexpressing C. glutamicum cells were found to be able to grow inthe presence of 20 μg/ml lincomycin. In contrast, cells which do notoverexpress LMRB (or cells carrying a LMRB disruption) were not able togrow on agar media containing 5 μg/ml lincomycin. This effect wasclearly visible in liquid culture. LMRB overexpression led to a 9-foldincreased resistance (compared to wild-type) against lincomycin and LMRBdisruption resulted in a decreased resistance (28% of wild-type) to thisantibiotic.

Example 12 Analysis of the Gene Sequences of the Invention

The comparison of sequences and determination of percent homologybetween two sequences are art-known techniques, and can be accomplishedusing a mathematical algorithm, such as the algorithm of Karlin andAltschul (1990) Proc. Natl. Acad. Sci. USA 87:2264-68, modified as inKarlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-77. Suchan algorithm is incorporated into the NBLAST and XBLAST programs(version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10. BLASTnucleotide searches can be performed with the NBLAST program, score=100,wordlength=12 to obtain nucleotide sequences homologous to SRT nucleicacid molecules of the invention. BLAST protein searches can be performedwith the XBLAST program, score=50, wordlength=3 to obtain amino acidsequences homologous to SRT protein molecules of the invention. Toobtain gapped alignments for comparison purposes, Gapped BLAST can beutilized as described in Altschul et al., (1997) Nucleic Acids Res.25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs, one ofordinary skill in the art will know how to optimize the parameters ofthe program (e.g., XBLAST and NBLAST) for the specific sequence beinganalyzed.

Another example of a mathematical algorithm utilized for the comparisonof sequences is the algorithm of Meyers and Miller ((1988) Comput. Appl.Biosci. 4: 11-17). Such an algorithm is incorporated into the ALIGNprogram (version 2.0) which is part of the GCG sequence alignmentsoftware package. When utilizing the ALIGN program for comparing aminoacid sequences, a PAM 120 weight residue table, a gap length penalty of12, and a gap penalty of 4 can be used. Additional algorithms forsequence analysis are known in the art, and include ADVANCE and ADAM.described in Torelli and Robotti (1994) Comput. Appl. Biosci. 10:3-5;and FASTA, described in Pearson and Lipman (1988) P.N.A.S. 85:2444-8.

The percent homology between two amino acid sequences can also beaccomplished using the GAP program in the GCG software package(available at http://www.gcg.com), using either a Blosum 62 matrix or aPAM250 matrix, and a gap weight of 12, 10, 8, 6, or 4 and a lengthweight of 2, 3, or 4. The percent homology between two nucleic acidsequences can be accomplished using the GAP program in the GCG softwarepackage, using standard parameters, such as a gap weight of 50 and alength weight of 3.

A comparative analysis of the gene sequences of the invention with thosepresent in Genbank has been performed using techniques known in the art(see, e.g., Bexevanis and Ouellette, eds. (1998) Bioinformatics: APractical Guide to the Analysis of Genes and Proteins. John Wiley andSons: New York). The gene sequences of the invention were compared togenes present in Genbank in a three-step process. In a first step, aBLASTN analysis (e.g., a local alignment analysis) was performed foreach of the sequences of the invention against the nucleotide sequencespresent in Genbank, and the top 500 hits were retained for furtheranalysis. A subsequent FASTA search (e.g., a combined local and globalalignment analysis, in which limited regions of the sequences arealigned) was performed on these 500 hits. Each gene sequence of theinvention was subsequently globally aligned to each of the top threeFASTA hits, using the GAP program in the GCG software package (usingstandard parameters). In order to obtain correct results, the length ofthe sequences extracted from Genbank were adjusted to the length of thequery sequences by methods well-known in the art. The results of thisanalysis are set forth in Table 4. The resulting data is identical tothat which would have been obtained had a GAP (global) analysis alonebeen performed on each of the genes of the invention in comparison witheach of the references in Genbank, but required significantly reducedcomputational time as compared to such a database-wide GAP (global)analysis. Sequences of the invention for which no alignments above thecutoff values were obtained are indicated on Table 4 by the absence ofalignment information. It will further be understood by one of ordinaryskill in the art that the GAP alignment homology percentages set forthin Table 4 under the heading “% homology (GAP)” are listed in theEuropean numerical format, wherein a ‘,’ represents a decimal point. Forexample, a value of “40,345” in this column represents “40.345%”.

Example 13 Construction and Operation of DNA Microarrays

The sequences of the invention may additionally be used in theconstruction and application of DNA microarrays (the design,methodology, and uses of DNA arrays are well known in the art, and aredescribed, for example, in Schena, M. et al. (1995) Science 270:467-470; Wodicka, L. et al. (1997) Nature Biotechnology 15: 1359-1367;DeSaizieu, A. et al. (1998) Nature Biotechnology 16: 45-48; and DeRisi,J. L. et al. (1997) Science 278: 680-686).

DNA microarrays are solid or flexible supports consisting ofnitrocellulose, nylon, glass, silicone, or other materials. Nucleic acidmolecules may be attached to the surface in an ordered manner. Afterappropriate labeling, other nucleic acids or nucleic acid mixtures canbe hybridized to the immobilized nucleic acid molecules, and the labelmay be used to monitor and measure the individual signal intensities ofthe hybridized molecules at defined regions. This methodology allows thesimultaneous quantification of the relative or absolute amount of all orselected nucleic acids in the applied nucleic acid sample or mixture.DNA microarrays, therefore, permit an analysis of the expression ofmultiple (as many as 6800 or more) nucleic acids in parallel (see, e.g.,Schena, M. (1996) BioEssays 18(5): 427-431).

The sequences of the invention may be used to design oligonucleotideprimers which are able to amplify defined regions of one or more C.glutamicum genes by a nucleic acid amplification reaction such as thepolymerase chain reaction. The choice and design of the 5′ or 3′oligonucleotide primers or of appropriate linkers allows the covalentattachment of the resulting PCR products to the surface of a supportmedium described above (and also described, for example, Schena, M. etal. (1995) Science 270: 467-470).

Nucleic acid microarrays may also be constructed by in situoligonucleotide synthesis as described by Wodicka, L. et al. (1997)Nature Biotechnology 15: 1359-1367. By photolithographic methods,precisely defined regions of the matrix are exposed to light. Protectivegroups which are photolabile are thereby activated and undergonucleotide addition, whereas regions that are masked from light do notundergo any modification. Subsequent cycles of protection and lightactivation permit the synthesis of different oligonucleotides at definedpositions. Small, defined regions of the genes of the invention may besynthesized on microarrays by solid phase oligonucleotide synthesis.

The nucleic acid molecules of the invention present in a sample ormixture of nucleotides may be hybridized to the microarrays. Thesenucleic acid molecules can be labeled according to standard methods. Inbrief, nucleic acid molecules (e.g., mRNA molecules or DNA molecules)are labeled by the incorporation of isotopically or fluorescentlylabeled nucleotides, e.g., during reverse transcription or DNAsynthesis. Hybridization of labeled nucleic acids to microarrays isdescribed (e.g., in Schena, M. et al. (1995) supra; Wodicka, L. et al.(1997), supra; and DeSaizieu A. et al. (1998), supra). The detection andquantification of the hybridized molecule are tailored to the specificincorporated label. Radioactive labels can be detected, for example, asdescribed in Schena, M. et al. (1995) supra) and fluorescent labels maybe detected, for example, by the method of Shalon et al. (1996) GenomeResearch 6: 639-645).

The application of the sequences of the invention to DNA microarraytechnology, as described above, permits comparative analyses ofdifferent strains of C. glutamicum or other Corynebacteria. For example,studies of inter-strain variations based on individual transcriptprofiles and the identification of genes that are important for specificand/or desired strain properties such as pathogenicity, productivity andstress tolerance are facilitated by nucleic acid array methodologies.Also, comparisons of the profile of expression of genes of the inventionduring the course of a fermentation reaction are possible using nucleicacid array technology.

Example 14 Analysis of the Dynamics of Cellular Protein Populations

(Proteomics)

The genes, compositions, and methods of the invention may be applied tostudy the interactions and dynamics of populations of proteins, termed‘proteomics’. Protein populations of interest include, but are notlimited to, the total protein population of C. glutamicum (e.g., incomparison with the protein populations of other organisms), thoseproteins which are active under specific environmental or metabolicconditions (e.g., during fermentation, at high or low temperature, or athigh or low pH), or those proteins which are active during specificphases of growth and development.

Protein populations can be analyzed by various well-known techniques,such as gel electrophoresis. Cellular proteins may be obtained, forexample, by lysis or extraction, and may be separated from one anotherusing a variety of electrophoretic techniques. Sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) separates proteins largelyon the basis of their molecular weight. Isoelectric focusingpolyacrylamide gel electrophoresis (IEF-PAGE) separates proteins bytheir isoelectric point (which reflects not only the amino acid sequencebut also posttranslational modifications of the protein). Another, morepreferred method of protein analysis is the consecutive combination ofboth IEF-PAGE and SDS-PAGE, known as 2-D-gel electrophoresis (described,for example, in Hermann et al. (1998) Electrophoresis 19: 3217-3221;Fountoulakis et al. (1998) Electrophoresis 19: 1193-1202; Langen et al.(1997) Electrophoresis 18: 1184-1192; Antelmann et al. (1997)Electrophoresis 18: 1451-1463). Other separation techniques may also beutilized for protein separation, such as capillary gel electrophoresis;such techniques are well known in the art.

Proteins separated by these methodologies can be visualized by standardtechniques, such as by staining or labeling. Suitable stains are knownin the art, and include Coomassie Brilliant Blue, silver stain, orfluorescent dyes such as Sypro Ruby (Molecular Probes). The inclusion ofradioactively labeled amino acids or other protein precursors (e.g.,³⁵S-methionine, ³⁵S-cysteine, ¹⁴C-labelled amino acids, ¹⁵N-amino acids,¹⁵NO₃ or ¹⁵NH₄ ⁺ or ¹³C-labelled amino acids) in the medium of C.glutamicum permits the labeling of proteins from these cells prior totheir separation. Similarly, fluorescent labels may be employed. Theselabeled proteins can be extracted, isolated and separated according tothe previously described techniques.

Proteins visualized by these techniques can be further analyzed bymeasuring the amount of dye or label used. The amount of a given proteincan be determined quantitatively using, for example, optical methods andcan be compared to the amount of other proteins in the same gel or inother gels. Comparisons of proteins on gels can be made, for example, byoptical comparison, by spectroscopy, by image scanning and analysis ofgels, or through the use of photographic films and screens. Suchtechniques are well-known in the art.

To determine the identity of any given protein, direct sequencing orother standard techniques may be employed. For example, N- and/orC-terminal amino acid sequencing (such as Edman degradation) may beused, as may mass spectrometry (in particular MALDI or ESI techniques(see, e.g., Langen et al. (1997) Electrophoresis 18: 1184-1192)). Theprotein sequences provided herein can be used for the identification ofC. glutamicum proteins by these techniques.

The information obtained by these methods can be used to comparepatterns of protein presence, activity, or modification betweendifferent samples from various biological conditions (e.g., differentorganisms, time points of fermentation, media conditions, or differentbiotopes, among others). Data obtained from such experiments alone, orin combination with other techniques, can be used for variousapplications, such as to compare the behavior of various organisms in agiven (e.g., metabolic) situation, to increase the productivity ofstrains which produce fine chemicals or to increase the efficiency ofthe production of fine chemicals.

EQUIVALENTS

Those of ordinary skill in the art will recognize, or will be able toascertain using no more than routine experimentation, many equivalentsto the specific embodiments of the invention described herein. Suchequivalents are intended to be encompassed by the following claims.TABLE 1 Genes Included in the Application Nucleic Acid Amino Acid SEQ IDNO SEQ ID NO Identification Code Contig. NT Start NT Stop Function 1 2RXA01524 GR00424 29041 30483 Lincomycine RESISTANCE PROTEIN 3 4 RXA00497GR00124 52 348 10 KD CHAPERONIN 5 6 RXN00493 VV0086 14389 16002 60 KDCHAPERONIN 7 8 F RXA00498 GR00124 363 1601 60 KD CHAPERONIN 9 10RXA01217 GR00353 802 203 GENERAL STRESS PROTEIN CTC 11 12 RXA00605GR00159 7412 5865 CATALASE (EC 1.11.1.6) 13 14 RXA00404 GR00089 2909 594CARBON STARVATION PROTEIN A 15 16 RXN03119 VV0098 86877 87008 SUPEROXIDEDISMUTASE [MN] (EC 1.15.1.1) 17 18 RXN03120 VV0098 87351 87476SUPEROXIDE DISMUTASE [MN] (EC 1.15.1.1) 19 20 RXN00575 VV0323 1471615252 PHOSPHINOTHRICIN-RESISTANCE PROTEIN 21 22 F RXA00575 GR00156 21301648 PHOSPHINOTHRICIN-RESISTANCE PROTEIN Chaperones 23 24 RXN01345VV0123 4883 3432 Moleculares chaperon (HSP70/DnaK family) 25 26 FRXA01345 GR00391 1172 6 Molecular chaperones (HSP70/DnaK family) 27 28RXA02541 GR00726 13657 12473 DNAJ PROTEIN 29 30 RXA02542 GR00726 1451813865 GRPE PROTEIN 31 32 RXN02543 VV0057 22031 20178 DNAK PROTEIN 33 34F RXA02543 GR00726 16375 14522 DNAK PROTEIN 35 36 RXN02280 VV0152 184926 TRAP1 37 38 F RXA02282 GR00659 1145 1480 Molecular chaperone, HSP90family 39 40 RXA00886 GR00242 12396 13541 DNAJ PROTEIN 41 42 RXS00568VV0251 2928 1582 TRIGGER FACTOR 43 44 RXN03038 VV0017 42941 43666 PS1PROTEIN VORLÄUFER 45 46 RXN03039 VV0018 2 631 PS1 PROTEIN VORLÄUFER 4748 RXN03040 VV0018 761 1069 PS1 PROTEIN VORLÄUFER 49 50 RXN03051 VV00222832 3566 PS1 PROTEIN VORLÄUFER 51 52 RXN03054 VV0026 1906 3486 PS1PROTEIN VORLÄUFER 53 54 RXN02949 VV0025 31243 31575 PREPROTEINTRANSLOKASE SECE UNTEREINHEIT 55 56 RXN02462 VV0124 11932 13749PREPROTEIN TRANSLOKASE SECA UNTEREINHEIT 57 58 RXN01559 VV0171 7795 5954PROTEIN-EXPORT MEMBRANE PROTEIN SECD 59 60 RXN00046 VV0119 5363 6058Signal Erkennung particle GTPase 61 62 RXN01863 VV0206 1172 24 /O/CThioredoxin-ähnliche oxidoreductase 63 64 RXN00833 VV0180 8039 8533THIOL PEROXIDASE (EC 1.11.1.—) 65 66 RXN01676 VV0179 12059 11304 THIOL:DISULFIDE AUSTAUSCH PROTEIN DSBD 67 68 RXN00380 VV0223 836 216 THIOL:DISULFIDE AUSTAUSCH PROTEIN TLPA 69 70 RXN00937 VV0079 42335 42706THIOREDOXIN 71 72 RXN02325 VV0047 5527 6393 THIOREDOXIN 73 74 RXN01837VV0320 7103 7879 PEPTIDYL-PROLYL CIS-TRANS ISOMERASE (EC 5.2.1.8) 75 76RXN01926 VV0284 1 741 PEPTID KETTE RELEASE FACTOR 3 77 78 RXN02002VV0111 141 518 PEPTID KETTE RELEASE FACTOR 3 79 80 RXN02736 VV0074 1360014556 PUTATIVES OXPPCYCLE PROTEIN OPCA 81 82 RXS03217 SMALL COLD-SHOCKPROTEIN 83 84 F RXA01917 GR00549 3465 3665 SMALL COLD-SHOCK PROTEINProteins involved in stress responses 85 86 RXA02184 GR00641 19628 19248COLD SHOCK-LIKE PROTEIN CSPC 87 88 RXA00810 GR00218 792 992 SMALLCOLD-SHOCK PROTEIN 89 90 RXA01674 GR00467 1878 2771 PROBABLE HYDROGENPEROXIDE-INDUCIBLE GENES ACTIVATOR 91 92 RXA02431 GR00708 2 1192damage-inducible protein P 93 94 RXA02446 GR00709 11640 11206OSMOTICALLY INDUCIBLE PROTEIN C 95 96 RXA02861 GR10006 551 1633 probablemetallothionein u0308aa - Mycobacterium leprae 97 98 RXA00981 GR002763388 4017 GTP PYROPHOSPHOKINASE (EC 2.7.6.5) 99 100 RXN00786 VV0321 1680706 LYTB PROTEIN 101 102 RXS01027 VV0143 5761 6768 DIADENOSINE5′,5′′′-P1,P4-TETRAPHOSPHATE HYDROLASE (EC 3.6.1.17) 103 104 RXS01528VV0050 17276 16749 DIADENOSINE 5′,5′′′-P1,P4-TETRAPHOSPHATE HYDROLASE(EC 3.6.1.17) 105 106 RXS01716 VV0319 3259 2774 EXOPOLYPHOSPHATASE (EC3.6.1.11) 107 108 RXS01835 VV0143 10575 10045GUANOSINE-3′,5′-BIS(DIPHOSPHATE) 3′-PYROPHOSPHOHYDROLASE (EC 3.1.7.2)109 110 RXS02497 VV0007 15609 16535 EXOPOLYPHOSPHATASE (EC 3.6.1.11) 111112 RXS02972 VV0319 2763 2353 EXOPOLYPHOSPHATASE (EC 3.6.1.11)Resistance and tolerance 113 114 RXA02159 GR00640 6231 6743 ARGININEHYDROXIMATE RESISTANCE PROTEIN 115 116 RXA02201 GR00646 5837 6199ARSENATE REDUCTASE 117 118 RXA00599 GR00159 1843 1457ARSENICAL-RESISTANCE PROTEIN ACR3 119 120 RXA00600 GR00159 2940 1843ARSENICAL-RESISTANCE PROTEIN ACR3 121 122 RXA02200 GR00646 4651 5760ARSENICAL-RESISTANCE PROTEIN ACR3 123 124 RXA02202 GR00646 6278 6916ARSENICAL-RESISTANCE PROTEIN ACR3 125 126 RXA02205 GR00646 9871 8993BACITRACIN RESISTANCE PROTEIN (PUTATIVE UNDECAPRENOL KINASE) (EC2.7.1.66) 127 128 RXA00900 GR00245 4052 3201 BICYCLOMYCIN RESISTANCEPROTEIN 129 130 RXN00901 VV0140 8581 8168 BICYCLOMYCIN RESISTANCEPROTEIN 131 132 F RXA00901 GR00245 4357 3980 BICYCLOMYCIN RESISTANCEPROTEIN 133 134 RXA00289 GR00046 3263 4438 CHLORAMPHENICOL RESISTANCEPROTEIN 135 136 RXN01984 VV0056 1515 1811 CHLORAMPHENICOL RESISTANCEPROTEIN 137 138 F RXA01984 GR00574 282 4 CHLORAMPHENICOL RESISTANCEPROTEIN 139 140 RXA00109 GR00015 1176 565 COPPER RESISTANCE PROTEIN CPRECURSOR 141 142 RXA00109 GR00015 1176 565 COPPER RESISTANCE PROTEIN CPRECURSOR 143 144 RXA00996 GR00283 1763 1023 DAUNORUBICIN RESISTANCEATP-BINDING PROTEIN DRRA 145 146 RXN00829 VV0180 7950 5611 DAUNORUBICINRESISTANCE PROTEIN 147 148 F RXA00829 GR00224 2 256 DAUNORUBICINRESISTANCE PROTEIN 149 150 F RXA00834 GR00225 463 2025 DAUNORUBICINRESISTANCE PROTEIN 151 152 RXA00995 GR00283 1023 283 DAUNORUBICINRESISTANCE TRANSMEMBRANE PROTEIN 153 154 RXN00803 VV0009 53858 52629METHYLENOMYCIN A RESISTANCE PROTEIN 155 156 F RXA00803 GR00214 4560 5162METHYLENOMYCIN A RESISTANCE PROTEIN 157 158 RXA01407 GR00410 3918 3028METHYLENOMYCIN A RESISTANCE PROTEIN 159 160 RXA01408 GR00410 4384 4184METHYLENOMYCIN A RESISTANCE PROTEIN 161 162 RXN01922 VV0020 2031 3182METHYLENOMYCIN A RESISTANCE PROTEIN 163 164 F RXA01922 GR00552 3 1109METHYLENOMYCIN A RESISTANCE PROTEIN 165 166 RXA02060 GR00626 1 339MYCINAMICIN-RESISTANCE PROTEIN MYRA 167 168 RXN01936 VV0127 40116 41387MACROLIDE-EFFLUX PROTEIN 169 170 F RXA01936 GR00555 9796 8975 NICKELRESISTANCE PROTEIN 171 172 F RXA01937 GR00555 10246 9821 NICKELRESISTANCE PROTEIN 173 174 RXN01010 VV0209 3776 4894 QUINOLONERESISTANCE NORA PROTEIN 175 176 F RXA01010 GR00288 774 4 QUINOLONERESISTANCE NORA PROTEIN 177 178 RXN03142 VV0136 5754 4612 QUINOLONERESISTANCE NORA PROTEIN 179 180 F RXA01150 GR00323 3807 2917 QUINOLONERESISTANCE NORA PROTEIN 181 182 RXN02964 VV0102 7931 6714 QUINOLONERESISTANCE NORA PROTEIN 183 184 F RXA02116 GR00636 911 6 QUINOLONERESISTANCE NORA PROTEIN 185 186 RXA00858 GR00233 1680 2147 TELLURIUMRESISTANCE PROTEIN TERC 187 188 RXA02305 GR00663 2921 2070 DAUNOMYCINC-14 HYDROXYLASE 189 190 RXA00084 GR00013 2367 1543 VIBRIOBACTINUTILIZATION PROTEIN VIUB 191 192 RXA00843 GR00228 3236 3580 ARSENATEREDUCTASE 193 194 RXA01052 GR00296 3398 3706 MERCURIC REDUCTASE (EC1.16.1.1) 195 196 RXA01053 GR00296 3772 4191 MERCURIC REDUCTASE (EC1.16.1.1) 197 198 RXA01054 GR00296 4229 4717 MERCURIC REDUCTASE (EC1.16.1.1) 199 200 RXN03123 VV0106 808 1245 HEAVY METAL TOLERANCE PROTEINPRECURSOR 201 202 F RXA00993 GR00282 641 6 HEAVY METAL TOLERANCE PROTEINPRECURSOR 203 204 RXA01051 GR00296 3298 2690 VANZ PROTEIN teicoplanin,resistance protein 205 206 RXN01873 VV0248 2054 819 Hypothetical DrugResistance Protein 207 208 F RXA01873 GR00535 855 1946 Hypothetical DrugResistance Protein 209 210 RXN00034 VV0020 16933 18381 MULTIDRUGRESISTANCE PROTEIN B 211 212 F RXA02273 GR00655 8058 9002 HypotheticalDrug Resistance Protein 213 214 RXN03075 VV0042 2491 3216 HypotheticalDrug Transporter 215 216 F RXA02907 GR10044 1395 2120 Hypothetical DrugTransporter 217 218 RXA00479 GR00119 16290 14101 Hypothetical DrugTransporter 219 220 RXN03124 VV0108 4 963 Hypothetical Drug Transporter221 222 F RXA01180 GR00336 4 765 Hypothetical Drug Transporter 223 224RXA02586 GR00741 10296 10027 Hypothetical Drug Transporter 225 226RXA02587 GR00741 12343 10253 Hypothetical Drug Transporter 227 228RXN03042 VV0018 2440 1835 Hypothetical Drug Transporter 229 230 FRXA02893 GR10035 1841 1236 Hypothetical Drug Transporter 231 232RXA01616 GR00450 1684 203 MULTIDRUG EFFLUX PROTEIN QACB 233 234 RXA01666GR00463 2307 3683 MULTIDRUG RESISTANCE PROTEIN 235 236 RXA00062 GR0000913252 11855 MULTIDRUG RESISTANCE PROTEIN B 237 238 RXA00215 GR0003213834 15294 MULTIDRUG RESISTANCE PROTEIN B 239 240 RXN03064 VV0038 48926223 MULTIDRUG RESISTANCE PROTEIN B 241 242 F RXA00565 GR00151 4892 5884MULTIDRUG RESISTANCE PROTEIN B 243 244 F RXA02878 GR10016 1837 1481MULTIDRUG RESISTANCE PROTEIN B 245 246 RXA00648 GR00169 2713 1304MULTIDRUG RESISTANCE PROTEIN B 247 248 RXN01320 VV0082 13146 11500MULTIDRUG RESISTANCE PROTEIN B 249 250 F RXA01314 GR00382 744 4MULTIDRUG RESISTANCE PROTEIN B 251 252 F RXA01320 GR00383 1979 1200MULTIDRUG RESISTANCE PROTEIN B 253 254 RXN02926 VV0082 11497 9866MULTIDRUG RESISTANCE PROTEIN B 255 256 F RXA01319 GR00383 1197 4MULTIDRUG RESISTANCE PROTEIN B 257 258 RXA01578 GR00439 1423 29MULTIDRUG RESISTANCE PROTEIN B 259 260 RXA02087 GR00629 7076 5730MULTIDRUG RESISTANCE PROTEIN B 261 262 RXA02088 GR00629 8294 7080MULTIDRUG RESISTANCE PROTEIN B 263 264 RXA00764 GR00204 3284 2169 BMRUPROTEIN Bacillus subtilis bmrU, multidrug efflux transporter 265 266RXN03125 VV0108 972 1142 Hypothetical Drug Transporter 267 268 RXN01553VV0135 25201 26520 Hypothetical Drug Permease 269 270 RXN00535 VV02195155 5871 Hypothetical Drug Resistance Protein 271 272 RXN00453 VV00761173 3521 Hypothetical Drug Transporter 273 274 RXN00932 VV0171 1312013593 Hypothetical Drug Transporter 275 276 RXN03022 VV0002 65 511MULTIDRUG RESISTANCE PROTEIN B 277 278 RXN03151 VV0163 489 4MYCINAMICIN-RESISTANCE PROTEIN MYRA 279 280 RXN02832 VV0358 547 5LYSOSTAPHIN IMMUNITY FACTOR 281 282 RXN00165 VV0232 3275 1860 MULTIDRUGRESISTANCE-LIKE ATP-BINDING PROTEIN MDL 283 284 RXN01190 VV0169 899210338 MULTIDRUG RESISTANCE-LIKE ATP-BINDING PROTEIN MDL 285 286 RXN01102VV0059 6128 4884 QUINOLONE RESISTANCE NORA PROTEIN 287 288 RXN00788VV0321 3424 3648 CHLORAMPHENICOL RESISTANCE PROTEIN 289 290 RXN02119VV0102 11242 9602 A201A-RESISTANCE ATP-BINDING PROTEIN 291 292 RXN01605VV0137 7124 5610 DAUNORUBICIN RESISTANCE TRANSMEMBRANE PROTEIN 293 294RXN01091 VV0326 567 4 MAZG PROTEIN 295 296 RXS02979 VV0149 2150 2383MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENT PRECURSOR 297 298RXS02987 VV0234 527 294 MERCURIC TRANSPORT PROTEIN PERIPLASMIC COMPONENTPRECURSOR 299 300 RXS03095 VV0057 4056 4424 CADMIUM EFFLUX SYSTEMACCESSORY PROTEIN HOMOLOG

GenBank ™ Gene Accession No. Name Gene Function Reference A09073 ppgPhosphoenol pyruvate carboxylase Bachmann, B. et al. “DNA fragmentcoding for phosphoenolpyruvat corboxylase, recombinant DNA carrying saidfragment, strains carrying the recombinant DNA and method for producingL-aminino acids using said strains,” Patent: EP 0358940-A 3 Mar. 21,1990 A45579, Threonine dehydratase Moeckel, B. et al. “Production ofL-isoleucine by means of recombinant A45581, micro-organisms withderegulated threonine dehydratase,” Patent: WO A45583, 9519442-A 5 Jul.20, 1995 A45585 A45587 AB003132 murC; Kobayashi, M. et al. “Cloning,sequencing, and characterization of the ftsZ ftsQ; gene from coryneformbacteria,” Biochem. Biophys. Res. Commun., ftsZ 236(2): 383-388 (1997)AB015023 murC; Wachi, M. et al. “A murC gene from Coryneform bacteria,”Appl. Microbiol. ftsQ Biotechnol., 51(2): 223-228 (1999) AB018530 dtsRKimura, E. et al. “Molecular cloning of a novel gene, dtsR, whichrescues the detergent sensitivity of a mutant derived fromBrevibacterium lactofermentum,” Biosci. Biotechnol. Biochem., 60(10):1565-1570 (1996) AB018531 dtsR1; dtsR2 AB020624 murI D-glutamateracemase AB023377 tkt transketolase AB024708 gltB; gltD Glutamine2-oxoglutarate aminotransferase large and small subunits AB025424 acnaconitase AB027714 rep Replication protein AB027715 rep; aad Replicationprotein; aminoglycoside adenyltransferase AF005242 argCN-acetylglutamate-5-semialdehyde dehydrogenase AF005635 glnA Glutaminesynthetase AF030405 hisF cyclase AF030520 argG Argininosuccinatesynthetase AF031518 argF Ornithine carbamolytransferase AF036932 aroD3-dehydroquinate dehydratase AF038548 pyc Pyruvate carboxylase AF038651dciAE; Dipeptide-binding protein; adenine Wehmeier, L. et al. “The roleof the Corynebacterium glutamicum rel gene in apt; relphosphoribosyltransferase; GTP (p)ppGpp metabolism,” Microbiology, 144:1853-1862 (1998) pyrophosphokinase AF041436 argR Arginine repressorAF045998 impA Inositol monophosphate phosphatase AF048764 argHArgininosuccinate lyase AF049897 argC; N-acetylglutamylphosphatereductase; argJ; ornithine acetyltransferase; N- argB; acetylglutamatekinase; acetylornithine argD; transminase; ornithine argF;carbamoyltransferase; arginine repressor; argR; argininosuccinatesynthase; argG; argininosuccinate lyase argH AF050109 inhA Enoyl-acylcarrier protein reductase AF050166 hisG ATP phosphoribosyltransferaseAF051846 hisA Phosphoribosylformimino-5-amino-1-phosphoribosyl-4-imidazolecarboxamide isomerase AF052652 metA HomoserineO-acetyltransferase Park, S. et al. “Isolation and analysis of metA, amethionine biosynthetic gene encoding homoserine acetyltransferase inCorynebacterium glutamicum,” Mol. Cells., 8(3): 286-294 (1998) AF053071aroB Dehydroquinate synthetase AF060558 hisH Glutamine amidotransferaseAF086704 hisE Phosphoribosyl-ATP- pyrophosphohydrolase AF114233 aroA5-enolpyruvylshikimate 3-phosphate synthase AF116184 panDL-aspartate-alpha-decarboxylase precursor Dusch, N. et al. “Expressionof the Corynebacterium glutamicum panD gene encodingL-aspartate-alpha-decarboxylase leads to pantothenate overproduction inEscherichia coli,” Appl. Environ. Microbiol., 65(4)1530-1539 (1999)AF124518 aroD; 3-dehydroquinase; shikimate aroE dehydrogenase AF124600aroC; Chorismate synthase; shikimate kinase; 3- aroK; dehydroquinatesynthase; putative aroB; cytoplasmic peptidase pepQ AF145897 inhAAF145898 inhA AJ001436 ectP Transport of ectoine, glycine betaine,Peter, H. et al. “Corynebacterium glutamicum is equipped with foursecondary proline carriers for compatible solutes: Identification,sequencing, and characterization of the proline/ectoine uptake system,ProP, and the ectoine/proline/glycine betaine carrier, EctP,” J.Bacteriol., 180(22): 6005-6012 (1998) AJ004934 dapDTetrahydrodipicolinate succinylase Wehrmann, A. et al. “Different modesof diaminopimelate synthesis and their (incomplete^(i)) role in cellwall integrity: A study with Corynebacterium glutamicum,” J. Bacteriol.,180(12): 3159-3165 (1998) AJ007732 ppc; secG;Phosphoenolpyruvate-carboxylase; ?; high amt; ocd; affinity ammoniumuptake protein; soxA putative ornithine-cyclodecarboxylase; sarcosineoxidase AJ010319 ftsY, Involved in cell division; PII protein; Jakoby,M. et al. “Nitrogen regulation in Corynebacterium glutamicum; glnB,uridylyltransferase (uridylyl-removing Isolation of genes involved inbiochemical characterization of corresponding glnD; srp; enzmye); signalrecognition particle; low proteins,” FEMS Microbiol., 173(2): 303-310(1999) amtP affinity ammonium uptake protein AJ132968 catChloramphenicol aceteyl transferase AJ224946 mqo L-malate: quinoneoxidoreductase Molenaar, D. et al. “Biochemical and geneticcharacterization of the membrane-associated malate dehydrogenase(acceptor) from Corynebacterium glutamicum,” Eur. J. Biochem., 254(2):395-403 (1998) AJ238250 ndh NADH dehydrogenase AJ238703 porA PorinLichtinger, T. et al. “Biochemical and biophysical characterization ofthe cell wall porin of Corynebacterium glutamicum: The channel is formedby a low molecular mass polypeptide,” Biochemistry, 37(43): 15024-15032(1998) D17429 Transposable element IS31831 Vertes, A. A. et al.“Isolation and characterization of IS31831, a transposable element fromCorynebacterium glutamicum,” Mol. 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“DNA fragment havingpromoter function in coryneform bacterium,” Patent: JP 1995031476-A 1Feb. 03, 1995 E08649 Aspartase Kohama, K. et al “DNA fragment havingpromoter function in coryneform bacterium,” Patent: JP 1995031478-A 1Feb. 03, 1995 E08900 Dihydrodipicolinate reductase Madori, M. et al.“DNA fragment containing gene coding Dihydrodipicolinate acid reductaseand utilization thereof,” Patent: JP 1995075578-A 1 Mar. 20, 1995 E08901Diaminopimelic acid decarboxylase Madori, M. et al. “DNA fragmentcontaining gene coding Diaminopimelic acid decarboxylase and utilizationthereof,” Patent: JP 1995075579-A 1 Mar. 20, 1995 E12594 Serinehydroxymethyltransferase Hatakeyama, K. et al. “Production ofL-trypophan,” Patent: JP 1997028391-A 1 Feb. 4, 1997 E12760, transposaseMoriya, M. et al. “Amplification of gene using artificial transposon,”Patent: E12759, JP 1997070291-A Mar. 18, 1997 E12758 E12764 Arginyl-tRNAsynthetase; diaminopimelic Moriya, M. et al. “Amplification of geneusing artificial transposon,” Patent: acid decarboxylase JP 1997070291-AMar. 18, 1997 E12767 Dihydrodipicolinic acid synthetase Moriya, M. etal. “Amplification of gene using artificial transposon,” Patent: JP1997070291-A Mar. 18, 1997 E12770 aspartokinase Moriya, M. et al.“Amplification of gene using artificial transposon,” Patent: JP1997070291-A Mar. 18, 1997 E12773 Dihydrodipicolinic acid reductaseMoriya, M. et al. “Amplification of gene using artificial transposon,”Patent: JP 1997070291-A Mar. 18, 1997 E13655 Glucose-6-phosphatedehydrogenase Hatakeyama, K. et al. “Glucose-6-phosphate dehydrogenaseand DNA capable of coding the same,” Patent: JP 1997224661-A 1 Sep. 02,1997 L01508 IlvA Threonine dehydratase Moeckel, B. et al. “Functionaland structural analysis of the threonine dehydratase of Corynebacteriumglutamicum,” J. Bacteriol., 174: 8065-8072 (1992) L07603 EC3-deoxy-D-arabinoheptulosonate-7- Chen, C. et al. “The cloning andnucleotide sequence of Corynebacterium 4.2.1.15 phosphate synthaseglutamicum 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase gene,”FEMS Microbiol. Lett., 107: 223-230 (1993) L09232 IlvB; Acetohydroxyacid synthase large subunit; Keilhauer, C. et al. “Isoleucine synthesisin Corynebacterium glutamicum: ilvN; Acetohydroxy acid synthase smallsubunit; molecular analysis of the ilvB-ilvN-ilvC operon,” J. ilvCAcetohydroxy acid isomeroreductase Bacteriol., 175(17): 5595-5603 (1993)L18874 PtsM Phosphoenolpyruvate sugar Fouet, A et al. “Bacillus subtilissucrose-specific enzyme II of the phosphotransferase phosphotransferasesystem: expression in Escherichia coli and homology to enzymes II fromenteric bacteria,” PNAS USA, 84(24): 8773-8777 (1987); Lee, J. K. et al.“Nucleotide sequence of the gene encoding the Corynebacterium glutamicummannose enzyme II and analyses of the deduced protein sequence,” FEMSMicrobiol. Lett., 119(1-2): 137-145 (1994) L27123 aceB Malate synthaseLee, H-S. et al. “Molecular characterization of aceB, a gene encodingmalate synthase in Corynebacterium glutamicum,” J. Microbiol.Biotechnol., 4(4): 256-263 (1994) L27126 Pyruvate kinase Jetten, M. S.et al. “Structural and functional analysis of pyruvate kinase fromCorynebacterium glutamicum,” Appl. Environ. Microbiol., 60(7): 2501-2507(1994) L28760 aceA Isocitrate lyase L35906 dtxr Diphtheria toxinrepressor Oguiza, J. A. et al. “Molecular cloning, DNA sequenceanalysis, and characterization of the Corynebacterium diphtheriae dtxRfrom Brevibacterium lactofermentum,” J. Bacteriol., 177(2): 465-467(1995) M13774 Prephenate dehydratase Follettie, M. T. et al. “Molecularcloning and nucleotide sequence of the Corynebacterium glutamicum pheAgene,” J. Bacteriol., 167: 695-702 (1986) M16175 5S rRNA Park, Y-H. etal. “Phylogenetic analysis of the coryneform bacteria by 56 rRNAsequences,” J. Bacteriol., 169: 1801-1806 (1987) M16663 trpEAnthranilate synthase, 5′ end Sano, K. et al. “Structure and function ofthe trp operon control regions of Brevibacterium lactofermentum, aglutamic-acid-producing bacterium,” Gene, 52: 191-200 (1987) M16664 trpATryptophan synthase, 3′end Sano, K. et al. “Structure and function ofthe trp operon control regions of Brevibacterium lactofermentum, aglutamic-acid-producing bacterium,” Gene, 52: 191-200 (1987) M25819Phosphoenolpyruvate carboxylase O'Regan, M. et al. “Cloning andnucleotide sequence of the Phosphoenolpyruvate carboxylase-coding geneof Corynebacterium glutamicum ATCC13032,” Gene, 77(2): 237-251 (1989)M85106 23S rRNA gene insertion sequence Roller, C. et al. “Gram-positivebacteria with a high DNA G + C content are characterized by a commoninsertion within their 23S rRNA genes,” J. Gen. Microbiol., 138:1167-1175 (1992) M85107, 23S rRNA gene insertion sequence Roller, C. etal. “Gram-positive bacteria with a high DNA G + C content are M85108characterized by a common insertion within their 23S rRNA genes,” J.Gen. Microbiol., 138: 1167-1175 (1992) M89931 aecD; Beta C-S lyase;branched-chain Rossol, I. et al. “The Corynebacterium glutamicum aecDgene encodes a C-S brnQ; amino acid uptake carrier; hypothetical lyasewith alpha, beta-elimination activity that degrades aminoethylcysteine,”yhbw protein yhbw J. Bacteriol., 174(9): 2968-2977 (1992); Tauch, A. etal. “Isoleucine uptake in Corynebacterium glutamicum ATCC 13032 isdirected by the brnQ gene product,” Arch. Microbiol., 169(4): 303-312(1998) S59299 trp Leader gene (promoter) Herry, D. M. et al. “Cloning ofthe trp gene cluster from a tryptophan- hyperproducing strain ofCorynebacterium glutamicum: identification of a mutation in the trpleader sequence,” Appl. Environ. Microbiol., 59(3): 791-799 (1993)U11545 trpD Anthranilate phosphoribosyltransferase O'Gara, J. P. andDunican, L. K. (1994) Complete nucleotide sequence of theCorynebacterium glutamicum ATCC 21850 tpD gene.” Thesis, MicrobiologyDepartment, University College Galway, Ireland. U13922 cglIM; Putativetype II 5-cytosoine Schafer, A. et al. “Cloning and characterization ofa DNA region encoding a cglIR; methyltransferase; putative type IIstress-sensitive restriction system from Corynebacterium glutamicum ATCCclgIIR restriction endonuclease; putative type I or 13032 and analysisof its role in intergeneric conjugation with Escherichia type IIIrestriction endonuclease coli,” J. Bacteriol., 176(23): 7309-7319(1994); Schafer, A. et al. “The Corynebacterium glutamicum cglIM geneencoding a 5-cytosine in an McrBC- deficient Escherichia coli strain,”Gene, 203(2): 95-101 (1997) U14965 recA U31224 ppx Ankri, S. et al.“Mutations in the Corynebacterium glutamicumproline biosyntheticpathway: A natural bypass of the proA step,” J. Bacteriol., 178(15):4412-4419 (1996) U31225 proC L-proline: NADP+ 5-oxidoreductase Ankri, S.et al. “Mutations in the Corynebacterium glutamicumproline biosyntheticpathway: A natural bypass of the proA step,” J. Bacteriol., 178(15):4412-4419 (1996) U31230 obg; proB; ?; gamma glutamyl kinase; similar toD- Ankri, S. et al. “Mutations in the Corynebacterium glutamicumprolineunkdh isomer specific 2-hydroxyacid biosynthetic pathway: A naturalbypass of the proA step,” J. Bacteriol., dehydrogenases 178(15):4412-4419 (1996) U31281 bioB Biotin synthase Serebriiskii, I. G., “Twonew members of the bio B superfamily: Cloning, sequencing and expressionof bio B genes of Methylobacillus flagellatum and Corynebacteriumglutamicum,” Gene, 175: 15-22 (1996) U35023 thtR; Thiosulfatesulfurtransferase; acyl CoA Jager, W. et al. “A Corynebacteriumglutamicum gene encoding a two-domain accBC carboxylase protein similarto biotin carboxylases and biotin-carboxyl-carrier proteins,” Arch.Microbiol., 166(2); 76-82 (1996) U43535 cmr Multidrug resistance proteinJager, W. et al. “A Corynebacterium glutamicum gene conferring multidrugresistance in the heterologous host Escherichia coli,” J. Bacteriol.,179(7): 2449-2451 (1997) U43536 clpB Heat shock ATP-binding proteinU53587 aphA-3 3′5″-aminoglycoside phosphotransferase U89648Corynebacterium glutamicum unidentified sequence involved in histidinebiosynthesis, partial sequence X04960 trpA; Tryptophan operon Matsui, K.et al. “Complete nucleotide and deduced amino acid sequences of trpB;the Brevibacterium lactofermentum tryptophan operon,” Nucleic AcidsRes., trpC; 14(24): 10113-10114 (1986) trpD; trpE; trpG; trpL X07563 lysA DAP decarboxylase (meso- Yeh, P. et al. “Nucleic sequence of the lysAgene of Corynebacterium diaminopimelate decarboxylase, glutamicum andpossible mechanisms for modulation of its expression,” Mol. EC 4.1.1.20)Gen. Genet., 212(1): 112-119 (1988) X14234 EC Phosphoenolpyruvatecarboxylase Eikmanns, B. J. et al. “The Phosphoenolpyruvate carboxylasegene of 4.1.1.31 Corynebacterium glutamicum: Molecular cloning,nucleotide sequence, and expression,” Mol. Gen. Genet., 218(2): 330-339(1989); Lepiniec, L. et al. “Sorghum Phosphoenolpyruvate carboxylasegene family: structure, function and molecular evolution,” Plant. Mol.Biol., 21 (3): 487-502 (1993) X17313 fda Fructose-bisphosphate aldolaseVon der Osten, C. H. et al. “Molecular cloning, nucleotide sequence andfine- structural analysis of the Corynebacterium glutamicum fda gene:structural comparison of C. glutamicum fructose-1, 6-biphosphatealdolase to class I and class II aldolases,” Mol. Microbiol., X53993dapA L-2, 3-dihydrodipicolinate synthetase (EC Bonnassie, S. et al.“Nucleic sequence of the dapA gene from 4.2.1.52) Corynebacteriumglutamicum,” Nucleic Acids Res., 18(21): 6421 (1990) X54223 AttB-relatedsite Cianciotto, N. et al. “DNA sequence homology between att B-relatedsites of Corynebacterium diphtheriae, Corynebacterium ulcerans,Corynebacterium glutamicum, and the attP site of lambdacorynephage,”FEMS. Microbiol, Lett., 66: 299-302 (1990) X54740 argS; lysAArginyl-tRNA synthetase; Marcel, T. et al. “Nucleotide sequence andorganization Diaminopimelate decarboxylase of the upstream region of theCorynebacterium glutamicum lysA gene,” Mol. Microbiol., 4(11): 1819-1830(1990) X55994 trpL; trpE Putative leader peptide; anthranilate Heery, D.M. et al. “Nucleotide sequence of the Corynebacterium glutamicumsynthase component 1 trpE gene,” Nucleic Acids Res., 18(23): 7138 (1990)X56037 thrC Threonine synthase Han, K. S. et al. “The molecularstructure of the Corynebacterium glutamicum threonine synthase gene,”Mol. Microbiol., 4(10): 1693-1702 (1990) X56075 attB- Attachment siteCianciotto, N. et al. “DNA sequence homology between att B-related sitesof related Corynebacterium diphtheriae, Corynebacterium ulcerans,Corynebacterium site glutamicum, and the attP site oflambdacorynephage,” FEMS. Microbiol, Lett., 66: 299-302 (1990) X57226lysC- Aspartokinase-alpha subunit; Kalinowski, J. et al. “Genetic andbiochemical analysis of the Aspartokinase alpha; Aspartokinase-betasubunit; aspartate beta from Corynebacterium glutamicum,” Mol.Microbiol., 5(5): 1197-1204 (1991); lysC- semialdehyde dehydrogenaseKalinowski, J. et al. “Aspartokinase genes lysC alpha and lysC betaoverlap beta; and are adjacent to the aspertate beta-semialdehydedehydrogenase gene asd in asd Corynebacterium glutamicum,” Mol. Gen.Genet., 224(3): 317-324 (1990) X59403 gap; Glyceraldehyde-3-phosphate;Eikmanns, B. J. “Identification, sequence analysis, and expression of apgk; tpi phosphoglycerate kinase; triosephosphate Corynebacteriumglutamicum gene cluster encoding the three glycolytic isomerase enzymesglyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, andtriosephosphate isomeras,” J. Bacteriol., 174(19): 6076-6086 (1992)X59404 gdh Glutamate dehydrogenase Bormann, E. R. et al. “Molecularanalysis of the Corynebacterium glutamicum gdh gene encoding glutamatedehydrogenase,” Mol. Microbiol., 6(3): 317-326 (1992) X60312 lysIL-lysine permease Seep-Feldhaus, A. H. et al. “Molecular analysis of theCorynebacterium glutamicum lysI gene involved in lysine uptake,” Mol.Microbiol., 5(12): 2995-3005 (1991) X66078 cop1 Ps1 protein Joliff, G.et al. “Cloning and nucleotide sequence of the csp1 gene encoding PS1,one of the two major secreted proteins of Corynebacterium glutamicum:The deduced N-terminal region of PS1 is similar to the Mycobacteriumantigen 85 complex,” Mol. Microbiol., 6(16): 2349-2362 (1992) X66112 gltCitrate synthase Eikmanns, B. J. et al. “Cloning sequence, expressionand transcriptional analysis of the Corynebacterium glutamicum gltA geneencoding citrate synthase,” Microbiol., 140: 1817-1828 (1994) X67737dapB Dihydrodipicolinate reductase X69103 csp2 Surface layer protein PS2Peyret, J. L. et al. “Characterization of the cspB gene encoding PS2, anordered surface-layer protein in Corynebacterium glutamicum,” Mol.Microbiol., 9(1): 97-109 (1993) X69104 IS3 related insertion elementBonamy, C. et al. “Identification of IS1206, a Corynebacteriumglutamicum IS3-related insertion sequence and phylogenetic analysis,”Mol. Microbiol., 14(3): 571-581 (1994) X70959 leuA Isopropylmalatesynthase Patek, M. et al. “Leucine synthesis in Corynebacteriumglutamicum: enzyme activities, structure of leuA, and effect of leuAinactivation on lysine synthesis,” Appl. Environ. Microbiol., 60(1):133-140 (1994) X71489 icd Isocitrate dehydrogenase (NADP+) Eikmanns, B.J. et al. “Cloning sequence analysis, expression, and inactivation ofthe Corynebacterium glutamicum icd gene encoding isocitratedehydrogenase and biochemical characterization of the enzyme,” J.Bacteriol., 177(3): 774-782 (1995) X72855 GDHA Glutamate dehydrogenase(NADP+) X75083, mtrA 5-methyltryptophan resistance Heery, D. M. et al.“A sequence from a tryptophan-hyperproducing strain of X70584Corynebacterium glutamicum encoding resistance to 5-methyltryptophan,”Biochem. Biophys. Res. Commun., 201(3): 1255-1262 (1994) X75085 recAFitzpatrick, R. et al. “Construction and characterization of recA mutantstrains of Corynebacterium glutamicum and Brevibacteriumlactofermentum,” Appl. Microbiol. Biotechnol., 42(4): 575-580 (1994)X75504 aceA; thiX Partial Isocitrate lyase;? Reinscheid, D. J. et al.“Characterization of the isocitrate lyase gene from Corynebacteriumglutamicum and biochemical analysis of the enzyme,” J. Bacteriol.,176(12): 3474-3483 (1994) X76875 ATPase beta-subunit Ludwig, W. et al.“Phylogenetic relationships of bacteria based on comparative sequenceanalysis of elongation factor Tu and ATP-synthase beta-subunit genes,”Antonie Van Leeuwenhoek, 64: 285-305 (1993) X77034 tuf Elongation factorTu Ludwig, W. et al. “Phylogenetic relationships of bacteria based oncomparative sequence analysis of elongation factor Tu and ATP-synthasebeta-subunit genes,” Antonie Van Leeuwenhoek, 64: 285-305 (1993) X77384recA Billman-Jacobe, H. “Nucleotide sequence of a recA gene fromCorynebacterium glutamicum,” DNA Seq., 4(6): 403-404 (1994) X78491 aceBMalate synthase Reinscheid, D. J. et al. “Malate synthase fromCorynebacterium glutamicum pta-ack operon encodingphosphotransacetylase: sequence analysis,” Microbiology, 140: 3099-3108(1994) X80629 16S rDNA 16S ribosomal RNA Rainey, F. A. et al.“Phylogenetic analysis of the genera Rhodococcus and Norcardia andevidence for the evolutionary origin of the genus Norcardia from withinthe radiation of Rhodococcus species,” Microbiol., 141: 523-528 (1995)X81191 gluA; Glutamate uptake system Kronemeyer, W. et al. “Structure ofthe gluABCD cluster encoding the gluB; glutamate uptake system ofCorynebacterium glutamicum,” J. Bacteriol., gluC; 177(5): 1152-1158(1995) gluD X81379 dapE Succinyldiaminopimelate desuccinylase Wehrmann,A. et al. “Analysis of different DNA fragments of Corynebacteriumglutamicum complementing dapE of Escherichia coli,” Microbiology, 40:3349-56 (1994) X82061 16S rDNA 16S ribosomal RNA Ruimy, R. et al.“Phylogeny of the genus Corynebacterium deduced from analyses ofsmall-subunit ribosomal DNA sequences,” Int. J. Syst. Bacteriol., 45(4):740-746 (1995) X82928 asd; lysC Aspartate-semialdehyde dehydrogenase; ?Serebrijski, I. et al. “Multicopy suppression by asd gene and osmoticstress- dependent complementation by heterologous proA in proA mutants,”J. Bacteriol., 177(24): 7255-7260 (1995) X82929 proA Gamma-glutamylphosphate reductase Serebrijski, I. et al. “Multicopy suppression by asdgene and osmotic stress- dependent complementation by heterologous proAin proA mutants,” J. Bacteriol., 177(24): 7255-7260 (1995) X84257 16SrDNA 16S ribosomal RNA Pascual, C. et al. “Phylogenetic analysis of thegenus Corynebacterium based on 16S rRNA gene sequences,” Int. J. Syst.Bacteriol., 45(4): 724-728 (1995) X85965 aroP; Aromatic amino acidpermease; ? Wehrmann, A. et al. “Functional analysis of sequencesadjacent to dapE of dapE Corynebacterium glutamicumproline reveals thepresence of aroP, which encodes the aromatic amino acid transporter,” J.Bacteriol., 177(20): 5991-5993 (1995) X86157 argB; Acetylglutamatekinase; N-acetyl-gamma- Sakanyan, V. et al. “Genes and enzymes of theacetyl cycle of arginine argC; glutamyl-phosphate reductase;biosynthesis in Corynebacterium glutamicum: enzyme evolution in theearly argD; acetylornithine aminotransferase; ornithine steps of thearginine pathway,” Microbiology, 142: 99-108 (1996) argF;carbamoyltransferase; glutamate N- argJ acetyltransferase X89084 pta;ackA Phosphate acetyltransferase; acetate kinase Reinscheid, D. J. etal. “Cloning, sequence analysis, expression and inactivation of theCorynebacterium glutamicum pta-ack operon encoding phosphotransacetylaseand acetate kinase,” Microbiology, 145: 503-513 (1999) X89850 attBAttachment site Le Marrec, C. et al. “Genetic characterization ofsite-specific integration functions of phi AAU2 infecting “Arthrobacteraureus C70,” J. Bacteriol., 178(7): 1996-2004 (1996) X90356 Promoterfragment F1 Patek, M. et al. “Promoters from Corynebacterium glutamicum:cloning, molecular analysis and search for a consensus motif,”Microbiology, 142: 1297-1309 (1996) X90357 Promoter fragment F2 Patek,M. et al. “Promoters from Corynebacterium glutamicum: cloning, molecularanalysis and search for a consensus motif,” Microbiology, 142: 1297-1309(1996) X90358 Promoter fragment F10 Patek, M. et al. “Promoters fromCorynebacterium glutamicum: cloning, molecular analysis and search for aconsensus motif,” Microbiology, 142: 1297-1309 (1996) X90359 Promoterfragment F13 Patek, M. et al. “Promoters from Corynebacteriumglutamicum: cloning, molecular analysis and search for a consensusmotif,” Microbiology, 142: 1297-1309 (1996) X90360 Promoter fragment F22Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,molecular analysis and search for a consensus motif,” Microbiology, 142:1297-1309 (1996) X90361 Promoter fragment F34 Patek, M. et al.“Promoters from Corynebacterium glutamicum: cloning, molecular analysisand search for a consensus motif,” Microbiology, 142: 1297-1309 (1996)X90362 Promoter fragment F37 Patek, M. et al. “Promoters fromCorynebacterium glutamicum: cloning, molecular analysis and search for aconsensus motif,” Microbiology, 142: 1297-1309 (1996) X90363 Promoterfragment F45 Patek, M. et al. “Promoters from Corynebacteriumglutamicum: cloning, molecular analysis and search for a consensusmotif,” Microbiology, 142: 1297-1309 (1996) X90364 Promoter fragment F64Patek, M. et al. “Promoters from Corynebacterium glutamicum: cloning,molecular analysis and search for a consensus motif,” Microbiology, 142:1297-1309 (1996) X90365 Promoter fragment F75 Patek, M. et al.“Promoters from Corynebacterium glutamicum: cloning, molecular analysisand search for a consensus motif,” Microbiology, 142: 1297-1309 (1996)X90366 Promoter fragment PF101 Patek, M. et al. “Promoters fromCorynebacterium glutamicum: cloning, molecular analysis and search for aconsensus motif,” Microbiology, 142: 1297-1309 (1996) X90367 Promoterfragment PF104 Patek, M. et al. “Promoters from Corynebacteriumglutamicum: cloning, molecular analysis and search for a consensusmotif,” Microbiology, 142: 1297-1309 (1996) X90368 Promoter fragmentPF109 Patek, M. et al. “Promoters from Corynebacterium glutamicum:cloning, molecular analysis and search for a consensus motif,”Microbiology, 142: 1297-1309 (1996) X93513 amt Ammonium transport systemSiewe, R. M. et al. “Functional and genetic characterization of the(methyl) ammonium uptake carrier of Corynebacterium glutamicum,” J.Biol. Chem., 271(10): 5398-5403 (1996) X93514 betP Glycine betainetransport system Peter, H. et al. “Isolation, characterization, andexpression of the Corynebacterium glutamicum betP gene, encoding thetransport system for the compatible solute glycine betaine,” J.Bacteriol., 178(17): 5229-5234 (1996) X95649 orf4 Patek, M. et al.“Identification and transcriptional analysis of the dapB-ORF2- dapA-ORF4operon of Corynebacterium glutamicum, encoding two enzymes involved inL-lysine synthesis,” Biotechnol. Lett., 19: 1113-1117 (1997) X96471lysE; lysG Lysine exporter protein; Lysine export Vrljic, M. et al. “Anew type of transporter with a new type of cellular regulator proteinfunction: L-lysine export from Corynebacterium glutamicum,” Mol.Microbiol., 22(5): 815-826 (1996) X96580 panB; 3-methyl-2-oxobutanoateSahm, H. et al. “D-pantothenate synthesis in Corynebacterium glutamicumand panC; hydroxymethyltransferase; pantoate-beta- use of panBC andgenes encoding L-valine synthesis for D-pantothenate xylB alanineligase; xylulokinase overproduction,” Appl. Environ. Microbiol., 65(5):1973-1979 (1999) X96962 Insertion sequence IS1207 and transposase X99289Elongation factor P Ramos, A. et al. “Cloning, sequencing and expressionof the gene encoding elongation factor P in the amino-acid producerBrevibacterium lactofermentum (Corynebacterium glutamicum ATCC 13869),”Gene, 198: 217-222 (1997) Y00140 thrB Homoserine kinase Mateos, L. M. etal. “Nucleotide sequence of the homoserine kinase (thrB) gene of theBrevibacterium lactofermentum,” Nucleic Acids Res., 15(9): 3922 (1987)Y00151 ddh Meso-diaminopimelate D-dehydrogenase Ishino, S. et al.“Nucleotide sequence of the meso-diaminopimelate D- (EC 1.4.1.16)dehydrogenase gene from Corynebacterium glutamicum,” Nucleic Acids Res.,15(9): 3917 (1987) Y00476 thrA Homoserine dehydrogenase Mateos, L. M. etal. “Nucleotide sequence of the homoserine dehydrogenase (thrA) gene ofthe Brevibacterium lactofermentum,” Nucleic Acids Res., 15(24): 10598(1987) Y00546 hom; thrB Homoserine dehydrogenase; homoserine Peoples, O.P. et al. “Nucleotide sequence and fine structural analysis of thekinase Corynebacterium glutamicum hom-thrB operon,” Mol. Microbiol.,2(1): 63-72 (1988) Y08964 murC; UPD-N-acetylmuramate-alanine ligase;Honrubia, M. P. et al. “Identification, characterization, andchromosomal ftsQ/divD; division initiation protein or cell divisionorganization of the ftsZ gene from Brevibacterium lactofermentum,” Mol.Gen. ftsZ protein; cell division protein Genet., 259(1): 97-104 (1998)Y09163 putP High affinity proline transport system Peter, H. et al.“Isolation of the putP gene of Corynebacterium glutamicumproline andcharacterization of a low-affinity uptake system for compatiblesolutes,” Arch. Microbiol., 168(2): 143-151 (1997) Y09548 pyc Pyruvatecarboxylase Peters-Wendisch, P. G. et al. “Pyruvate carboxylase fromCorynebacterium glutamicum: characterization, expression andinactivation of the pyc gene,” Microbiology, 144: 915-927 (1998) Y09578leuB 3-isopropylmalate dehydrogenase Patek, M. et al. “Analysis of theleuB gene from Corynebacterium glutamicum,” Appl. Microbiol.Biotechnol., 50(1): 42-47 (1998) Y12472 Attachment site bacteriophagePhi-16 Moreau, S. et al. “Site-specific integration of corynephagePhi-16: The construction of an integration vector,” Microbiol., 145:539-548 (1999) Y12537 proP Proline/ectoine uptake system protein Peter,H. et al. “Corynebacterium glutamicum is equipped with four secondarycarriers for compatible solutes: Identification, sequencing, andcharacterization of the proline/ectoine uptake system, ProP, and theectoine/proline/glycine betaine carrier, EctP,” J. Bacteriol., 180(22):6005-6012 (1998) Y13221 glnA Glutamine synthetase I Jakoby, M. et al.“Isolation of Corynebacterium glutamicum glnA gene encoding glutaminesynthetase I,” FEMS Microbiol. Lett., 154(1): 81-88 (1997) Y16642 lpdDihydrolipoamide dehydrogenase Y18059 Attachment site Corynephage 304LMoreau, S. et al. “Analysis of the integration functions of &phi; 304L:An integrase module among corynephages,” Virology, 255(1): 150-159(1999) Z21501 argS; lysA Arginyl-tRNA synthetase; Oguiza, J. A. et al.“A gene encoding arginyl-tRNA synthetase diaminopimelate decarboxylaseis located in the upstream region of the lysA gene in Brevibacterium(partial) lactofermentum: Regulation of argS-lysA cluster expression byarginine,” J. Bacteriol., 175(22): 7356-7362 (1993) Z21502 dapA;Dihydrodipicolinate synthase; Pisabarro, A. et al. “A cluster of threegenes (dapA, orf2, and dapB) of dapB dihydrodipicolinate reductaseBrevibacterium lactofermentum encodes dihydrodipicolinate reductase, anda third polypeptide of unknown function,” J. Bacteriol., 175(9):2743-2749 (1993) Z29563 thrC Threonine synthase Malumbres, M. et al.“Analysis and expression of the thrC gene of the encoded threoninesynthase,” Appl. Environ. Microbiol., 60(7)2209-2219 (1994) Z46753 16SrDNA Gene for 16S ribosomal RNA Z49822 sigA SigA sigma factor Oguiza, J.A. et al “Multiple sigma factor genes in Brevibacterium lactofermentum:Characterization of sigA and sigB,” J. Bacteriol., 178(2): 550-553(1996) Z49823 galE; dtxR Catalytic activity UDP-galactose 4- Oguiza, J.A. et al “The galE gene encoding the UDP-galactose 4-epimerase ofepimerase; diphtheria toxin regulatory Brevibacterium lactofermentum iscoupled transcriptionally to the dmdR protein gene,” Gene, 177: 103-107(1996) Z49824 orfl; sigB ?; SigB sigma factor Oguiza, J. A. et al“Multiple sigma factor genes in Brevibacterium lactofermentum:Characterization of sigA and sigB,” J. Bacteriol., 178(2): 550-553(1996) Z66534 Transposase Correia, A. et al. “Cloning andcharacterization of an IS-like element present in the genome ofBrevibacterium lactofermentum ATCC 13869,” Gene, 170(1): 91-94 (1996)¹A sequence for this gene was published in the indicated reference.However, the sequence obtained by the inventors of the presentapplication is significantly longer than the published version. It isbelieved that the published version relied on an incorrect start codon,and thus represents only a fragment of the actual coding region.

TABLE 3 Corynebacterium and Brevibacterium Strains Which May be Used inthe Practice of the Invention Genus species ATCC FERM NRRL CECT NCIMBCBS NCTC DSMZ Brevibacterium ammoniagenes 21054 Brevibacteriumammoniagenes 19350 Brevibacterium ammoniagenes 19351 Brevibacteriumammoniagenes 19352 Brevibacterium ammoniagenes 19353 Brevibacteriumammoniagenes 19354 Brevibacterium ammoniagenes 19355 Brevibacteriumammoniagenes 19356 Brevibacterium ammoniagenes 21055 Brevibacteriumammoniagenes 21077 Brevibacterium ammoniagenes 21553 Brevibacteriumammoniagenes 21580 Brevibacterium ammoniagenes 39101 Brevibacteriumbutanicum 21196 Brevibacterium divaricatum 21792 P928 Brevibacteriumflavum 21474 Brevibacterium flavum 21129 Brevibacterium flavum 21518Brevibacterium flavum B11474 Brevibacterium flavum B11472 Brevibacteriumflavum 21127 Brevibacterium flavum 21128 Brevibacterium flavum 21427Brevibacterium flavum 21475 Brevibacterium flavum 21517 Brevibacteriumflavum 21528 Brevibacterium flavum 21529 Brevibacterium flavum B11477Brevibacterium flavum B11478 Brevibacterium flavum 21127 Brevibacteriumflavum B11474 Brevibacterium healii 15527 Brevibacterium ketoglutamicum21004 Brevibacterium ketoglutamicum 21089 Brevibacterium ketosoreductum21914 Brevibacterium lactofermentum 70 Brevibacterium lactofermentum 74Brevibacterium lactofermentum 77 Brevibacterium lactofermentum 21798Brevibacterium lactofermentum 21799 Brevibacterium lactofermentum 21800Brevibacterium lactofermentum 21801 Brevibacterium lactofermentum B11470Brevibacterium lactofermentum B11471 Brevibacterium lactofermentum 21086Brevibacterium lactofermentum 21420 Brevibacterium lactofermentum 21086Brevibacterium lactofermentum 31269 Brevibacterium linens 9174Brevibacterium linens 19391 Brevibacterium linens 8377 Brevibacteriumparaffinolyticum 11160 Brevibacterium spec. 717.73 Brevibacterium spec.717.73 Brevibacterium spec. 14604 Brevibacterium spec. 21860Brevibacterium spec. 21864 Brevibacterium spec. 21865 Brevibacteriumspec. 21866 Brevibacterium spec. 19240 Corynebacterium acetoacidophilum21476 Corynebacterium acetoacidophilum 13870 Corynebacteriumacetoglutamicum B11473 Corynebacterium acetoglutamicum B11475Corynebacterium acetoglutamicum 15806 Corynebacterium acetoglutamicum21491 Corynebacterium acetoglutamicum 31270 Corynebacterium acetophilumB3671 Corynebacterium ammoniagenes 6872 2399 Corynebacteriumammoniagenes 15511 Corynebacterium fujiokense 21496 Corynebacteriumglutamicum 14067 Corynebacterium glutamicum 39137 Corynebacteriumglutamicum 21254 Corynebacterium glutamicum 21255 Corynebacteriumglutamicum 31830 Corynebacterium glutamicum 13032 Corynebacteriumglutamicum 14305 Corynebacterium glutamicum 15455 Corynebacteriumglutamicum 13058 Corynebacterium glutamicum 13059 Corynebacteriumglutamicum 13060 Corynebacterium glutamicum 21492 Corynebacteriumglutamicum 21513 Corynebacterium glutamicum 21526 Corynebacteriumglutamicum 21543 Corynebacterium glutamicum 13287 Corynebacteriumglutamicum 21851 Corynebacterium glutamicum 21253 Corynebacteriumglutamicum 21514 Corynebacterium glutamicum 21516 Corynebacteriumglutamicum 21299 Corynebacterium glutamicum 21300 Corynebacteriumglutamicum 39684 Corynebacterium glutamicum 21488 Corynebacteriumglutamicum 21649 Corynebacterium glutamicum 21650 Corynebacteriumglutamicum 19223 Corynebacterium glutamicum 13869 Corynebacteriumglutamicum 21157 Corynebacterium glutamicum 21158 Corynebacteriumglutamicum 21159 Corynebacterium glutamicum 21355 Corynebacteriumglutamicum 31808 Corynebacterium glutamicum 21674 Corynebacteriumglutamicum 21562 Corynebacterium glutamicum 21563 Corynebacteriumglutamicum 21564 Corynebacterium glutamicum 21565 Corynebacteriumglutamicum 21566 Corynebacterium glutamicum 21567 Corynebacteriumglutamicum 21568 Corynebacterium glutamicum 21569 Corynebacteriumglutamicum 21570 Corynebacterium glutamicum 21571 Corynebacteriumglutamicum 21572 Corynebacterium glutamicum 21573 Corynebacteriumglutamicum 21579 Corynebacterium glutamicum 19049 Corynebacteriumglutamicum 19050 Corynebacterium glutamicum 19051 Corynebacteriumglutamicum 19052 Corynebacterium glutamicum 19053 Corynebacteriumglutamicum 19054 Corynebacterium glutamicum 19055 Corynebacteriumglutamicum 19056 Corynebacterium glutamicum 19057 Corynebacteriumglutamicum 19058 Corynebacterium glutamicum 19059 Corynebacteriumglutamicum 19060 Corynebacterium glutamicum 19185 Corynebacteriumglutamicum 13286 Corynebacterium glutamicum 21515 Corynebacteriumglutamicum 21527 Corynebacterium glutamicum 21544 Corynebacteriumglutamicum 21492 Corynebacterium glutamicum B8183 Corynebacteriumglutamicum B8182 Corynebacterium glutamicum B12416 Corynebacteriumglutamicum B12417 Corynebacterium glutamicum B12418 Corynebacteriumglutamicum B11476 Corynebacterium glutamicum 21608 Corynebacteriumlilium P973 Corynebacterium nitrilophilus 21419 11594 Corynebacteriumspec. P4445 Corynebacterium spec. P4446 Corynebacterium spec. 31088Corynebacterium spec. 31089 Corynebacterium spec. 31090 Corynebacteriumspec. 31090 Corynebacterium spec. 31090 Corynebacterium spec. 1595420145 Corynebacterium spec. 21857 Corynebacterium spec. 21862Corynebacterium spec. 21863ATCC: American Type Culture Collection, Rockville, MD, USAFERM: Fermentation Research Institute, Chiba, JapanNRRL: ARS Culture Collection, Northern Regional Research Laboratory,Peoria, IL, USACECT: Coleccion Espanola de Cultivos Tipo, Valencia, SpainNCIMB: National Collection of Industrial and Marine Bacteria Ltd.,Aberdeen, UKCBS: Centraalbureau voor Schimmelcultures, Baarn, NLNCTC: National Collection of Type Cultures, London, UKDSMZ: Deutsche Sammlung von Mikroorganismen und Zellkulturen,Braunschweig, GermanyFor reference see Sugawara, H. et al. (1993) World directory ofcollections of cultures of microorganisms: Bacteria, fungi and yeasts(4^(th) edn), World federation for culture collections world data centeron microorganisms, Saimata, Japen.

TABLE 4 ALIGNMENT RESULTS % ho- length mology Date of ID # (NT) GenbankHit Length Accession Name of Genbank Hit Source of Genbank Hit (GAP)Deposit rxa00062 1521 GB_HTG2:AC007366 185001 AC007366 Homo sapiensclone NH0501G22, *** SEQUENCING IN PROGRESS ***, 3 unordered Homosapiens 39,080 5-Jun-99 pieces. rxa00084 948 GB_PR3:HSU80741 912 U80741Homo sapiens CAGH44 mRNA, partial cds. Homo sapiens 39,264 18-DEC-1997GB_PL1:BNDNATRNA 1732 X89901 B. nigra DNA for tRNA like gene. Brassicanigra 36,725 6-Feb-97 GB_PR3:HSU80741 912 U80741 Homo sapiens CAGH44mRNA, partial cds. Homo sapiens 38,957 18-DEC-1997 rxa00109 735GB_GSS9:AQ163721 388 AQ163721 HS_2245_A1_F07_MF CIT Approved HumanGenomic Sperm Library D Homo Homo sapiens 45,066 16-OCT-1998 sapiensgenomic clone Plate = 2245 Col = 13 Row = K, genomic survey sequence.GB_HTG4:AC007054 171979 AC007054 Drosophila melanogaster chromosome 2clone BACR45O18 (D527) RPCI-98 45.O.18 Drosophila melanogaster 36,58913-OCT-1999 map 41E-41E strain y; cn bw sp, *** SEQUENCING INPROGRESS***, 13 unordered pieces. GB_HTG4:AC007054 171979 AC007054Drosophila melanogaster chromosome 2 clone BACR45O18 (D527) RPCI-9845.O.18 Drosophila melanogaster 36,589 13-OCT-1999 map 41E-41E strain y;cn bw sp, *** SEQUENCING IN PROGRESS***, 13 unordered pieces. rxa002151449 GB_BA1:SC9C7 31360 AL035161 Streptomyces coelicolor cosmid 9C7.Streptomyces coelicolor 44,444 12-Jan-99 GB_BA1:SCE94 38532 AL049628Streptomyces coelicolor cosmid E94. Streptomyces coelicolor 36,31312-Apr-99 GB_BA2:AF110185 20302 AF110185 Burkholderia pseudomalleistrain 1026b DbhB (dbhB), general secretory pathway Burkholderiapseudomallei 44,159 2-Aug-99 protein D (gspD), general secretory pathwayprotein E (gspE), general secretory pathway protein F (gspF), GspC(gspC), general secretory pathway protein G (gspG), general secretorypathway protein H (gspH), general secretory pathway protein I (gspI),general secretory pathway protein J (gspJ), general secretory pathwayprotein K (gspK), general secretory pathway protein L (gspL), generalsecretory pathway protein M (gspM), and general secretory pathwayprotein N (gspN) genes, complete cds; and unknown genes. rxa00289 1299GB_EST6:N80167 384 N80167 za65g02.s1 Soares fetal liver spleen 1NFLSHomo sapiens cDNA clone IMAGE: 297458 Homo sapiens 40,420 29-MAR-19963′, mRNA sequence. GB_STS:G37084 384 G37084 SHGC-56832 Human Homosapiens STS genomic, sequence tagged site. Homo sapiens 40,42030-MAR-1998 GB_STS:G37084 384 G37084 SHGC-56832 Human Homo sapiens STSgenomic, sequence tagged site. Homo sapiens 40,420 30-MAR-1998 rxa004042439 GB_BA1:MTCY22D7 31859 Z83866 Mycobacterium tuberculosis H37Rvcomplete genome; segment 133/162. Mycobacterium 60,271 17-Jun-98tuberculosis GB_BA1:ECU82598 136742 U82598 Escherichia coli genomicsequence of minutes 9 to 12. Escherichia coli 54,256 15-Jan-97GB_BA2:AE000165 12003 AE000165 Escherichia coli K-12 MG1655 section 55of 400 of the complete genome. Escherichia coli 54,256 12-Nov-98rxa00479 2313 GB_BA1:SCF43A 35437 AL096837 Streptomyces coelicolorcosmid F43A. Streptomyces coelicolor 36,245 13-Jul-99 A3(2)GB_GSS2:CNS015U4 1036 AL105910 Drosophila melanogaster genome surveysequence SP6 end of BAC BACN14G08 of Drosophila melanogaster 37,57326-Jul-99 DrosBAC library from Drosophila melanogaster (fruit fly),genomic survey sequence. GB_PR3:HSA494O16 50502 AL117328 Human DNAsequence from clone 494O16 on chromosome 22, complete sequence. Homosapiens 36,475 23-Nov-99 rxa00497 420 GB_BA1:MTCY78 33818 Z77165Mycobacterium tuberculosis H37Rv complete genome; segment 145/162.Mycobacterium 40,250 17-Jun-98 tuberculosis GB_BA2:AF079544 817 AF079544Mycobacterium avium GroESL operon, partial sequence. Mycobacterium avium64,439 16-Aug-98 rxa00575 GB_BA1:MTGROEOP 2987 X60350 M. tuberculosisgroE gene for KCS and 10-kDa products. Mycobacterium 62,857 23-Apr-92tuberculosis rxa00599 510 GB_GSS10:AQ199703 439 AQ199703 RPCI11-46O13.TJRPCI-11 Homo sapiens genomic clone RPCI-11-46O13, genomic Homo sapiens42,657 20-Apr-99 survey sequence. GB_PR2:AC002127 144165 AC002127 HumanBAC clone RG305H12 from 7q21, complete sequence. Homo sapiens 37,05227-MAY-1997 GB_STS:G51234 439 G51234 SHGC-80708 Human Homo sapiens STSgenomic, sequence tagged site. Homo sapiens 42,657 25-Jun-99 rxa006001221 GB_BA1:MTCY441 35187 Z80225 Mycobacterium tuberculosis H37Rvcomplete genome; segment 118/162. Mycobacterium 56,183 18-Jun-98tuberculosis GB_BA1:MSGY223 42061 AD000019 Mycobacterium tuberculosissequence from clone y223. Mycobacterium 37,217 10-DEC-1996 tuberculosisGB_BA1:BSUB0014 213420 Z99117 Bacillus subtilis complete genome (section14 of 21): from 2599451 to 2812870. Bacillus subtilis 36,553 26-Nov-97rxa00605 1603 GB_BA2:AF069070 2776 AF069070 Endosymbiont of Onchocercavolvulus catalase gene, complete cds. endosymbiont of 55,396 25-Nov-98Onchocerca volvulus GB_BA1:OVCAT 1845 X82176 Onchocerca volvulusendobacterial mRNA for catalase. endosymbiont of 55,396 26-Nov-98Onchocerca volvulus GB_BA1:SC2G5 38404 AL035478 Streptomyces coelicolorcosmid 2G5. Streptomyces coelicolor 39,530 11-Jun-99 rxa00648 1533GB_HTG1:HS74O16 169401 AL110119 Homo sapiens chromosome 21 cloneRPCIP704O1674 map 21q21, *** SEQUENCING Homo sapiens 36,327 27-Aug-99 INPROGRESS ***, in unordered pieces. GB_HTG1:HS74O16 169401 AL110119 Homosapiens chromosome 21 clone RPCIP704O1674 map 21q21, *** SEQUENCING Homosapiens 36,327 27-Aug-99 IN PROGRESS ***, in unordered pieces.GB_HTG1:HS74O16 169401 AL110119 Homo sapiens chromosome 21 cloneRPCIP704O1674 map 21q21, *** SEQUENCING Homo sapiens 35,119 27-Aug-99 INPROGRESS ***, in unordered pieces. rxa00764 1239 GB_EST36:AI898007 609AI898007 EST267450 tomato ovary, TAMU Lycopersicon esculentum cDNA clonecLED31K22, Lycopersicon esculentum 34,323 27-Jul-99 mRNA sequence.GB_BA2:PAU93274 8008 U93274 Pseudomonas aeruginosa YafE (yafE), LeuB(leuB), Asd (asd), FimV (fimV), and HisT Pseudomonas aeruginosa 35,89523-Jun-98 (hisT) genes, complete cds; TrpF (trpF) gene, partial cds; andunknown gene. GB_BA2:PAU93274 8008 U93274 Pseudomonas aeruginosa YafE(yafE), LeuB (leuB), Asd (asd), FimV (fimV), and HisT Pseudomonasaeruginosa 41,417 23-Jun-98 (hisT) genes, complete cds; TrpF (trpF)gene, partial cds; and unknown gene. rxa00803 1353 GB_IN2:CELH34C0327748 AF100662 Caenorhabditis elegans cosmid H34C03. Caenorhabditiselegans 34,152 28-OCT-1998 GB_HTG2:AC007905 100722 AC007905 Homo sapienschromosome 16q24.3 clone PAC 754F23, *** SEQUENCING IN Homo sapiens37,472 24-Jun-99 PROGRESS ***, 33 unordered pieces. GB_HTG2:AC007905100722 AC007905 Homo sapiens chromosome 16q24.3 clone PAC 754F23, ***SEQUENCING IN Homo sapiens 37,472 24-Jun-99 PROGRESS ***, 33 unorderedpieces. rxa00810 324 GB_BA1:MTY15C10 33050 Z95436 Mycobacteriumtuberculosis H37Rv complete genome; segment 154/162. Mycobacterium34,615 17-Jun-98 tuberculosis GB_BA1:MLCB2548 38916 AL023093Mycobacterium leprae cosmid B2548. Mycobacterium leprae 34,615 27-Aug-99GB_BA1:ECOUW76 225419 U00039 E. coli chromosomal region from 76.0 to81.5 minutes. Escherichia coli 52,997 7-Nov-96 rxa00829 2463GB_BA1:SC5C7 41906 AL031515 Streptomyces coelicolor cosmid 5C7.Streptomyces coelicolor 65,269 7-Sep-98 GB_BA1:SC5F2A 40105 AL049587Streptomyces coelicolor cosmid 5F2A. Streptomyces coelicolor 37,49024-MAY-1999 GB_BA1:STMDRRC 3374 L76359 Streptomyces peucetiusdaunorubicin resistance protein (drrC) gene, complete cds. Streptomycespeucetius 55,279 24-DEC-1996 rxa00843 468 GB_BA1:MTCY9C4 15916 Z77250Mycobacterium tuberculosis H37Rv complete genome; segment 113/162.Mycobacterium 40,000 17-Jun-98 tuberculosis GB_BA1:MTCY9C4 15916 Z77250Mycobacterium tuberculosis H37Rv complete genome; segment 113/162.Mycobacterium 37,773 17-Jun-98 tuberculosis rxa00858 568 GB_BA1:SCC5430753 AL035591 Streptomyces coelicolor cosmid C54. Streptomycescoelicolor 39,602 11-Jun-99 GB_EST18:N96610 547 N96610 21285 Lambda-PRL1Arabidopsis thaliana cDNA clone F10G3T7, mRNA sequence. Arabidopsisthaliana 37,801 5-Jan-98 GB_EST18:T45493 436 T45493 8756 Lambda-PRL2Arabidopsis thaliana cDNA clone 133C14T7, mRNA sequence. Arabidopsisthaliana 34,194 4-Aug-98 rxa00886 1269 GB_BA1:SYCSLLLH 132106 D64006Synechocystis sp. PCC6803 complete genome, 25/27, 3138604-3270709.Synechocystis sp. 37,459 13-Feb-99 GB_BA1:SCDNAJ 5611 X77458 S.coelicolor dnaK, grpE and dnaJ genes. Streptomyces coelicolor 49,74421-Nov-96 GB_BA1:STMDNAK 4648 L46700 Streptomyces coelicolor (strainA3(2)) dnaK operon encoding molecular chaperones Streptomyces coelicolor49,583 22-Nov-96 (dnaK, dnaJ), grpE and hspR genes, complete cds's.rxa00900 975 GB_BA2:ECOUW67_0 110000 U18997 Escherichia coli K-12chromosomal region from 67.4 to 76.0 minutes. Escherichia coli 38,314U18997 GB_BA2:ECOUW67_0 110000 U18997 Escherichia coli K-12 chromosomalregion from 67.4 to 76.0 minutes. Escherichia coli 37,759 U18997GB_BA2:AE000393 10516 AE000393 Escherichia coli K-12 MG1655 section 283of 400 of the complete genome. Escherichia coli 38,314 12-Nov-98rxa00901 537 GB_HTG3:AC010757 175571 AC010757 Homo sapiens chromosome 18clone 128_C_18 map 18, *** SEQUENCING IN Homo sapiens 34,857 22-Sep-99PROGRESS ***, 20 unordered pieces. GB_HTG3:AC010757 175571 AC010757 Homosapiens chromosome 18 clone 128_C_18 map 18, *** SEQUENCING IN Homosapiens 34,857 22-Sep-99 PROGRESS ***, 20 unordered pieces.GB_HTG3:AC011283 87295 AC011283 Homo sapiens clone MS2016A09, ***SEQUENCING IN PROGRESS ***, 1 unordered Homo sapiens 35,448 07-OCT-1999pieces. rxa00981 753 GB_OV:GGA245664 512 AJ245664 Gallus gallus partialmRNA for ATP-citrate lyase (ACL gene). Gallus gallus 37,538 28-Sep-99GB_PL2:AC007887 159434 AC007887 Genomic sequence for Arabidopsisthaliana BAC F15O4 from chromosome I, complete Arabidopsis thaliana37,600 04-OCT-1999 sequence. GB_GSS1:CNS00RNW 542 AL087338 Arabidopsisthaliana genome survey sequence T7 end of BAC F14D7 of IGF libraryArabidopsis thaliana 41,264 28-Jun-99 from strain Columbia ofArabidopsis thaliana, genomic survey sequence. rxa00995 864GB_EST29:AI553951 450 AI553951 te54d01.x1 Soares_NFL_T_GBC_S1 Homosapiens cDNA clone IMAGE: 2090497 3′ Homo sapiens 42,627 13-Apr-99similar to gb: X02067 Homo sapiens mRNA for 7SL RNA pseudogene (HUMAN);,mRNA sequence. GB_PR3:AC003029 139166 AC003029 Homo sapiens Chromosome12q24 PAC RPCI3-462E2 (Roswell Park Cancer Institute Homo sapiens 38,91517-Sep-98 Human PAC library) complete sequence. GB_BA1:EAY14603 4479Y14603 Erwinia amylovora srlA, srlE, srlB, srlD, srlM and srlR genes.Erwinia amylovora 37,694 6-Jan-98 rxa00996 864 GB_BA2:AE001001 10730AE001001 Archaeoglobus fulgidus section 106 of 172 of the completegenome. Archaeoglobus fulgidus 41,078 15-DEC-1997 GB_EST30:AV018764 242AV018764 AV018764 Mus musculus 18-day embryo C57BL/6J Mus musculus cDNAclone Mus musculus 39,669 28-Aug-99 1190006M16, mRNA sequence.GB_GSS3:B24189 377 B24189 F19E16TF IGF Arabidopsis thaliana genomicclone F19E16, genomic survey sequence. Arabidopsis thaliana 44,38510-OCT-1997 rxa01010 1242 GB_OV:AF007068 356 AF007068 Coturnix coturnixarylalkylamine N-acetyltransferase mRNA, partial cds. Coturnix coturnix46,629 12-Jul-97 GB_EST10:AA166324 514 AA166324 ms50c09.r1 Life Techmouse embryo 13 5dpc 10666014 Mus musculus cDNA clone Mus musculus38,677 19-DEC-1996 IMAGE: 614992 5′ similar to SW: NEST_RAT P21263NESTIN.;, mRNA sequence. GB_EST7:W89968 46 W89968 mf64g11.r1 Soaresmouse embryo NbME13.5 14.5 Mus musculus cDNA clone Mus musculus 58,69612-Sep-96 IMAGE: 419108 5′ similar to SW: NEST_RAT P21263 NESTIN. [1];,mRNA sequence. rxa01051 732 GB_GSS12:AQ381423 579 AQ381423RPCI11-135F10.TJ RPCI-11 Homo sapiens genomic clone RPCI-11-135F10,genomic Homo sapiens 37,651 21-MAY-1999 survey sequence.GB_HTG6:AC010901 206121 AC010901 Homo sapiens clone RP11-544J22, WORKINGDRAFT SEQUENCE, 1 unordered Homo sapiens 36,011 04-DEC-1999 pieces.GB_GSS5:AQ746932 837 AQ746932 HS_5538_A1_A11_T7A RPCI-11 Human Male BACLibrary Homo sapiens genomic Homo sapiens 38,640 19-Jul-99 clone Plate =1114 Col = 21 Row = A, genomic survey sequence. rxa01052 432GB_IN1:CELC13D9 43487 AF016420 Caenorhabditis elegans cosmid C13D9.Caenorhabditis elegans 39,344 2-Aug-97 GB_IN1:CELC13D9 43487 AF016420Caenorhabditis elegans cosmid C13D9. Caenorhabditis elegans 38,7802-Aug-97 rxa01053 543 GB_OV:CHKMAFG1 1316 D28601 Chicken novelmaf-related gene mafG encoding bZip nuclear protein MafG, promoterGallus gallus 39,205 7-Feb-99 region and exon 1. GB_HTG6:AC010765 146468AC010765 Homo sapiens clone RP11-115N6, *** SEQUENCING IN PROGRESS ***,26 Homo sapiens 32,961 07-DEC-1999 unordered pieces. GB_HTG6:AC010765146468 AC010765 Homo sapiens clone RP11-115N6, *** SEQUENCING INPROGRESS ***, 26 Homo sapiens 38,476 07-DEC-1999 unordered pieces.rxa01054 612 GB_PL1:PHNPNGLP 962 D45425 Pharbitis nil mRNA for Pharbitisnil Germin-like protein precursor, complete cds. Ipomoea nil 42,92510-Feb-99 GB_HTG2:HSJ402N21 170302 AL049553 Homo sapiens chromosome 6clone RP3-402N21 map p21.1-21.31, ***SEQUENCING Homo sapiens 36,82503-DEC-1999 IN PROGRESS ***, in unordered pieces. GB_HTG2:HSJ402N21170302 AL049553 Homo sapiens chromosome 6 clone RP3-402N21 mapp21.1-21.31, ***SEQUENCING Homo sapiens 36,825 03-DEC-1999 IN PROGRESS***, in unordered pieces. rxa01217 723 GB_IN2:CELF18A12 29784 AF016688Caenorhabditis elegans cosmid F18A12. Caenorhabditis elegans 35,79408-OCT-1999 GB_IN2:CELF18A12 29784 AF016688 Caenorhabditis eleganscosmid F18A12. Caenorhabditis elegans 40,625 08-OCT-1999 GB_RO:MUSMCFTR6304 M60493 Mouse cystic fibrosis transmembrane conductance regulator(CFTR) mRNA, complete Mus musculus 37,793 10-Jun-94 cds. rxa01320 1770GB_BA2:AF031037 1472 AF031037 Neisseria meningitidis chloramphenicolacetyltransferase gene, complete cds. Neisseria meningitidis 35,01421-Apr-98 GB_HTG1:PFMAL13PA 80518 AL109815 Plasmodium falciparumchromosome 13 strain 3D7, *** SEQUENCING IN PROGRESS Plasmodiumfalciparum 17,697 19-Aug-99 ***, in unordered pieces. GB_HTG1:PFMAL13PA80518 AL109815 Plasmodium falciparum chromosome 13 strain 3D7, ***SEQUENCING IN PROGRESS Plasmodium falciparum 17,697 19-Aug-99 ***, inunordered pieces. rxa01345 1575 GB_PR3:AC005224 166687 AC005224 Homosapiens chromosome 17, clone hRPK.214_O_1, complete sequence. Homosapiens 38,195 14-Aug-98 GBPR3:AC005224 166687 AC005224 Homo sapienschromosome 17, clone hRPK.214_O_1, complete sequence. Homo sapiens36,611 14-Aug-98 GB_HTG3:AC011500_1 300851 AC011500 Homo sapienschromosome 19 clone CIT978SKB_60E11, *** SEQUENCING IN Homo sapiens36,446 AC011500 PROGRESS ***, 246 unordered pieces. rxa01407 1014GB_HTG3:AC010831 70233 AC010831 Homo sapiens clone 6_L_24, LOW-PASSSEQUENCE SAMPLING. Homo sapiens 35,764 23-Sep-99 GB_HTG3:AC010831 70233AC010831 Homo sapiens clone 6_L_24, LOW-PASS SEQUENCE SAMPLING. Homosapiens 35,764 23-Sep-99 GB_PR3:AC004058 38400 AC004058 Homo sapienschromosome 4 clone B241P19 map 4q25, complete sequence. Homo sapiens40,778 30-Sep-98 rxa01408 324 GB_PR4:AF152365 246546 AF152365 Homosapiens constitutive fragile region FRA3B sequence. Homo sapiens 41,2341-Aug-99 GB_HTG3:AC007890 121256 AC007890 Drosophila melanogasterchromosome 3 clone BACR02G21 (D722) RPCI-98 02.G.21 Drosophilamelanogaster 39,432 3-Sep-99 map 90E-91A strain y; cn bw sp, ***SEQUENCING IN PROGRESS***, 89 unordered pieces. GB_HTG3:AC007890 121256AC007890 Drosophila melanogaster chromosome 3 clone BACR02G21 (D722)RPCI-98 02.G.21 Drosophila melanogaster 39,432 3-Sep-99 map 90E-91Astrain y; cn bw sp, *** SEQUENCING IN PROGRESS***, 89 unordered pieces.rxa01524 1566 GB_BA1:BSUB0015 218410 Z99118 Bacillus subtilis completegenome (section 15 of 21): from 2795131 to 3013540. Bacillus subtilis38,201 26-Nov-97 GB_HTG2:AC008260 107439 AC008260 Drosophilamelanogaster chromosome 2 clone BACR13J10 (D924) RPCI-98 13.J.10Drosophila melanogaster 38,302 2-Aug-99 map 47B-47C strain y; cn bw sp,*** SEQUENCING IN PROGRESS***, 82 unordered pieces. GB_HTG2:AC008260107439 AC008260 Drosophila melanogaster chromosome 2 clone BACR13J10(D924) RPCI-98 13.J.10 Drosophila melanogaster 38,302 2-Aug-99 map47B-47C strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 82 unorderedpieces. rxa01578 1510 GB_PR4:AF111170 148083 AF111170 Homo sapiens 14q32Jagged2 gene, complete cds; and unknown gene. Homo sapiens 37,87314-Jul-99 GB_PR4:AF111170 148083 AF111170 Homo sapiens 14q32 Jagged2gene, complete cds; and unknown gene. Homo sapiens 40,220 14-Jul-99GB_BA1:AEY13732 6740 Y13732 Alcaligenes eutrophus genes for ureases,ureD1, ureD2, ureA, ureB, and ORF1, ORF2. Raistonia eutropha 42,96023-Sep-97 rxa01616 1605 GB_BA2:AF088857 2908 AF088857 Vogesellaindigofera indigoidine biosynthesis regulatory locus, complete sequence.Vogesella indigofera 37,626 10-Sep-99 GB_IN1:CEM04D8 21552 Z32682Caenorhabditis elegans cosmid M04D8, complete sequence. Caenorhabditiselegans 37,237 23-Nov-98 GB_EST25:AI281910 276 AI281910 qt82d04.x1NCI_CGAP_Co14 Homo sapiens cDNA clone IMAGE: 1961767 3′, mRNA Homosapiens 38,406 21-DEC-1998 sequence. rxa01666 1500 GB_BA1:CGU43535 2531U43535 Corynebacterium glutamicum multidrug resistance protein (cmr)gene, complete cds. Corynebacterium 99,933 9-Apr-97 glutamicumGB_HTG3:AC009213 114735 AC009213 Drosophila melanogaster chromosome 3clone BACR09F18 (D812) RPCI-98 09.F.18 Drosophila melanogaster 36,11123-Aug-99 map 98D-98D strain y; cn bw sp, *** SEQUENCING IN PROGRESS***, 109 unordered pieces. GB_HTG3:AC009213 114735 AC009213 Drosophilamelanogaster chromosome 3 clone BACR09F18 (D812) RPCI-98 09.F.18Drosophila melanogaster 36,111 23-Aug-99 map 98D-98D strain y; cn bw sp,*** SEQUENCING IN PROGRESS***, 109 unordered pieces. rxa01674 1017GB_PL1:AB017159 1859 AB017159 Daucus carota mRNA for citrate synthase,complete cds. Daucus carota 39,537 01-MAY-1999 GB_PR1:HUMGNOS48 23142D26607 Homo sapiens endothelial nitric oxide synthase gene, completecds. Homo sapiens 36,419 13-Jul-99 GB_HTG3:AC011234 154754 AC011234 Homosapiens clone NH0166D23, *** SEQUENCING IN PROGRESS ***, 7 unorderedHomo sapiens 36,317 04-OCT-1999 pieces. rxa01873 1359 GB_HTG3:AC009450124337 AC009450 Homo sapiens chromosome 9 clone 30_C_23 map 9, ***SEQUENCING IN Homo sapiens 35,303 22-Aug-99 PROGRESS ***, 20 unorderedpieces. GB_HTG3:AC009450 124337 AC009450 Homo sapiens chromosome 9 clone30_C_23 map 9, *** SEQUENCING IN Homo sapiens 35,303 22-Aug-99 PROGRESS***, 20 unordered pieces. GB_HTG3:AC009919 134724 AC009919 Homo sapiensclone 115_I_23, LOW-PASS SEQUENCE SAMPLING. Homo sapiens 35,409 8-Sep-99rxa01922 1275 GB_BA1:ECONEUC 1676 M84026 E. coli protein p7 (neu C)gene, complete cds. Escherichia coli 35,189 26-Apr-93 GB_HTG2:AC007853116280 AC007853 Drosophila melanogaster chromosome 3 clone BACR03L02(D766) RPCI-98 03.L.2 Drosophila melanogaster 34,365 2-Aug-99 map96B-96C strain y; cn bw sp, *** SEQUENCING IN PROGRESS ***, 80 unorderedpieces. GB_HTG2:AC007853 116280 AC007853 Drosophila melanogasterchromosome 3 clone BACR03L02 (D766) RPCI-98 03.L.2 Drosophilamelanogaster 34,365 2-Aug-99 map 96B-96C strain y; cn bw sp, ***SEQUENCING IN PROGRESS***, 80 unordered pieces. rxa01936 1395GB_HTG4:AC010037 166249 AC010037 Drosophila melanogaster chromosome3L/66B6 clone RPCI98-6E4, *** SEQUENCING Drosophila melanogaster 38,53416-OCT-1999 IN PROGRESS ***, 52 unordered pieces. GB_HTG4:AC010037166249 AC010037 Drosophila melanogaster chromosome 3L/66B6 cloneRPCI98-6E4, *** SEQUENCING Drosophila melanogaster 38,534 16-OCT-1999 INPROGRESS ***, 52 unordered pieces. GB_PR4:AC005552 167228 AC005552 Homosapiens chromosome 17, clone hRPK.212_E_8, complete sequence. Homosapiens 36,249 26-Nov-98 rxa01984 420 GB_PR1:HS169C8F 245 Z57239 Homosapiens CpG island DNA genomic Mse1 fragment, clone 169c8, forward readHomo sapiens 45,679 18-OCT-1995 cpg169c8.ft1a. GB_BA1:SERATTBXIS 3255L11597 Saccharopolyspora erythraea excisionase (xis) gene, integrase(int) gene, complete Saccharopolyspora 36,232 6-Jul-94 cds's and attBsite. erythraea rxa02060 GB_EST7:W97557 267 W97557 mf98a09.r1 Soaresmouse embryo NbME13.5 14.5 Mus musculus cDNA clone Mus musculus 42,96916-Jul-96 IMAGE: 422296 5′, mRNA sequence. rxa02087 1470 GB_PR3:AC005544169045 AC005544 Homo sapiens chromosome 17, clone hRPK.349_A_8, completesequence. Homo sapiens 35,724 25-Sep-98 GB_PL1:ATF20B18 104738 AL049483Arabidopsis thaliana DNA chromosome 4, BAC clone F20B18 (ESSA project).Arabidopsis thaliana 35,890 24-MAR-1999 GB_PL2:ATT25K17 89904 AL049171Arabidopsis thaliana DNA chromosome 4, BAC clone (ESSA project).Arabidopsis thaliana 38,128 27-Aug-99 rxa02088 1338 GB_HTG3:AC008697167932 AC008697 Homo sapiens chromosome 5 clone CIT978SKB_70D3, ***SEQUENCING IN Homo sapiens 36,662 3-Aug-99 PROGRESS ***, 54 unorderedpieces. GB_HTG3:AC008697 167932 AC008697 Homo sapiens chromosome 5 cloneCIT978SKB_70D3, *** SEQUENCING IN Homo sapiens 36,662 3-Aug-99 PROGRESS***, 54 unordered pieces. GB_HTG3:AC008703 213971 AC008703 Homo sapienschromosome 5 clone CIT978SKB_76P12, *** SEQUENCING IN Homo sapiens34,768 3-Aug-99 PROGRESS ***, 54 unordered pieces. rxa02159 636GB_BA2:AF049897 9196 AF049897 Corynebacterium glutamicumN-acetylglutamylphosphate reductase (argC), ornithine Corynebacterium99,843 1-Jul-98 acetyltransferase (argJ), N-acetylglutamate kinase(argB), acetylornithine transaminase glutamicum (argD), ornithinecarbamoyltransferase (argF), arginine repressor (argR),argininosuccinate synthase (argG), and argininosuccinate lyase (argH)genes, complete cds. GB_BA2:AF031518 2045 AF031518 Corynebacteriumglutamicum ornithine carbamolytransferase (argF) gene, complete cds.Corynebacterium 88,679 5-Jan-99 glutamicum GB_BA2:AF041436 516 AF041436Corynebacterium glutamicum arginine repressor (argR) gene, complete cds.Corynebacterium 100,000 5-Jan-99 glutamicum rxa02184 504 GB_BA1:BSZ929538164 Z92953 B. subtilis yws[A, B, C] genes and rbs[A, C, D, K, R] genes.Bacillus subtilis 38,951 24-Jun-98 GB_EST36:AI878071 593 AI878071fc57a12.y1 Zebrafish WashU MPIMG EST Danio rerio cDNA 5′ similar to TR:Q13151 Danio rerio 36,774 21-Jul-99 Q13151 HETEROGENEOUS NUCLEARRIBONUCLEOPROTEIN A0;, mRNA sequence. GB_EST37:AI958166 641 AI958166fc91f01.y1 Zebrafish WashU MPIMG EST Danio rerio cDNA 5′ similar to TR:Q13151 Danio rerio 36,774 20-Aug-99 Q13151 HETEROGENEOUS NUCLEARRIBONUCLEOPROTEIN A0;, mRNA sequence. rxa02200 1233 GB_PR3:HSA494O1650502 AL117328 Human DNA sequence from clone 494O16 on chromosome 22,complete sequence. Homo sapiens 38,648 23-Nov-99 GB_HTG2:AC008161 158440AC008161 Mus musculus clone 182_H_5, *** SEQUENCING IN PROGRESS ***, 29unordered Mus musculus 35,938 28-Jul-99 pieces. GB_HTG2:AC008161 158440AC008161 Mus musculus clone 182_H_5, *** SEQUENCING IN PROGRESS ***, 29unordered Mus musculus 35,938 28-Jul-99 pieces. rxa02201 486GB_EST4:H16949 465 H16949 ym34a11.r1 Soares infant brain 1NIB Homosapiens cDNA clone IMAGE: 50010 5′, Homo sapiens 38,267 29-Jun-95 mRNAsequence. GB_EST4:H16949 465 H16949 ym34a11.r1 Soares infant brain 1NIBHomo sapiens cDNA clone IMAGE: 50010 5′, Homo sapiens 36,552 29-Jun-95mRNA sequence. rxa02202 762 GB_IN1:CELC41A3 37149 U41541 Caenorhabditiselegans cosmid C41A3. Caenorhabditis elegans 41,678 08-DEC-1995GB_EST33:AV080151 236 AV080151 AV080151 Mus musculus stomach C57BL/6Jadult Mus musculus cDNA clone Mus musculus 43,348 25-Jun-99 2210413B04,mRNA sequence. GB_GSS5:AQ766877 545 AQ766877 HS_2017_B2_B08_MR CITApproved Human Genomic Sperm Library D Homo Homo sapiens 35,56828-Jul-99 sapiens genomic clone Plate = 2017 Col = 16 Row = D, genomicsurvey sequence. rxa02205 1002 GB_HTG2:AC005959 127587 AC005959 Homosapiens, *** SEQUENCING IN PROGRESS ***, 2 ordered pieces. Homo sapiens40,310 11-Nov-98 GB_HTG2:AC005959 127587 AC005959 Homo sapiens, ***SEQUENCING IN PROGRESS ***, 2 ordered pieces. Homo sapiens 40,31011-Nov-98 GB_IN1:BRPTUBBA 4571 M36380 B. pahangi beta-tubulin gene,complete cds. Brugla pahangi 37,703 26-Apr-93 rxa02305 975 GB_RO:MUSPAFR1140 D50872 Mouse gene for platelet activating factor receptor, completecds. Mus musculus 38,420 10-Feb-99 GB_PR3:HUMARL1A 1008 L28997 Homosapiens ARL1 mRNA, complete cds. Homo sapiens 42,188 13-Jan-95GB_BA1:MLCB2533 40245 AL035310 Mycobacterium leprae cosmid B2533.Mycobacterium leprae 42,000 27-Aug-99 rxa02431 899 GB_EST4:H35255 407H35255 EST111890 Rat PC-12 cells, NGF-treated (9 days) Rattus sp. cDNAclone RPNCO03, Rattus sp. 39,098 2-Apr-98 mRNA sequence.GB_HTG1:HS791K14 155318 AL035685 Homo sapiens chromosome 20 cloneRP4-791K14, *** SEQUENCING IN PROGRESS Homo sapiens 39,456 23-Nov-99***, in unordered pieces. GB_HTG1:HS791K14 155318 AL035685 Homo sapienschromosome 20 clone RP4-791K14, *** SEQUENCING IN PROGRESS Homo sapiens39,456 23-Nov-99 ***, in unordered pieces. rxa02446 558 GB_BA2:AF036166895 AF036166 Xanthomonas campestris organic hydroperoxide resistanceprotein (ohr) gene, complete Xanthomonas campestris 49,369 19-MAY-1998cds. GB_EST5:N25122 620 N25122 yx19d10.r1 Soares melanocyte 2NbHM Homosapiens cDNA clone IMAGE: 262195 5′, Homo sapiens 35,417 28-DEC-1995mRNA sequence. GB_EST5:N25122 620 N25122 yx19d10.r1 Soares melanocyte2NbHM Homo sapiens cDNA clone IMAGE: 262195 5′, Homo sapiens 37,17228-DEC-1995 mRNA sequence. rxa02541 1308 GB_BA2:DPU93358 1267 U93358Deinococcus proteolyticus 40 kDa heat shock chaperone protein (dnaJ)gene, complete Deinococcus proteolyticus 42,115 17-Jan-98 cds.GB_EST30:AI658096 343 AI658096 fc14c09.y1 Zebrafish WashU MPIMG ESTDanio rerio cDNA 5′ similar to Danio rerio 52,059 06-MAY-1999 SW:DNJ2_HUMAN P31689 DNAJ PROTEIN HOMOLOG 2.;, mRNA sequence.GB_EST37:AI959242 545 AI959242 fd25h11.y1 Zebrafish WashU MPIMG ESTDanio rerio cDNA 5′ similar to Danio rerio 45,438 20-Aug-99 SW:DNJ2_HUMAN P31689 DNAJ PROTEIN HOMOLOG 2.;, mRNA sequence. rxa02542 777EM_PAT:E10832 1856 E10832 DNA encoding Dnak protein which is one of heatshock protein from Corynebacterium 99,000 08-OCT-97 glutamicum (Rel. 52,Created) GB_EST24:Z82017 396 Z82017 SSZ82017 Porcine small intestinecDNA library Sus scrofa cDNA clone c12c06 5′ Sus scrofa 37,067 30-Apr-99similar to eukaryotic initiation factor 4 gamma, mRNA sequence.GB_OM:CATERYTHRO 681 L10606 Cat erythropoietin mRNA, 3′ end. Felis catus39,409 14-OCT-1993 rxa02543 1977 EM_PAT:E10832 1856 E10832 DNA encodingDnak protein which is one of heat shock protein from Corynebacterium97,306 08-OCT-1997 glutamicum (Rel. 52, Created) GB_BA1:MPHSP70 2179X59437 M. paratuberculosis gene for 70 kD heat shock protein.Mycobacterium avium 73,404 23-Apr-92 subsp. paratuberculosisGB_BA1:MTY13E10 35019 Z95324 Mycobacterium tuberculosis H37Rv completegenome; segment 18/162. Mycobacterium 72,028 17-Jun-98 tuberculosisrxa02586 393 GB_IN2:AC006472 156362 AC006472 Drosophila melanogaster,chromosome 2R, region 45E1-46A2, BAC clone Drosophila melanogaster37,958 30-Jan-99 BACR48G21, complete sequence. GB_HTG4:AC010020 106541AC010020 Drosophila melanogaster chromosome 3L/66D10 clone RPCI98-26I3,Drosophila melanogaster 37,333 16-OCT-1999 *** SEQUENCING IN PROGRESS***, 55 unordered pieces. GB_HTG4:AC010020 106541 AC010020 Drosophilamelanogaster chromosome 3L/66D10 clone RPCI98-26I3, Drosophilamelanogaster 37,333 16-OCT-1999 *** SEQUENCING IN PROGRESS ***, 55unordered pieces. rxa02587 2214 GB_BA1:MLCL622 42498 Z95398Mycobacterium leprae cosmid L622. Mycobacterium leprae 39,848 24-Jun-97GB_RO:AF074879 3316 AF074879 Rattus norvegicus testis-specific proteinTSPY gene, complete cds. Rattus norvegicus 35,830 6-Jul-99GB_RO:RNJ001380 2641 AJ001380 Rattus norvegicus Tspy partial genomicsequence, exons 1-6. Rattus norvegicus 37,702 29-Jun-98 rxs03217 331GB_BA1:MLCB2548 38916 AL023093 Mycobacterium leprae cosmid B2548.Mycobacterium leprae 37,888 27-Aug-99 GB_HTG2:HSJ662M14 174772 AL079336Homo sapiens chromosome 20 clone RP4-662M14, *** SEQUENCING IN PROGRESSHomo sapiens 36,420 4-Feb-00 ***, 10 unordered pieces. GB_HTG2:HSJ662M14174772 AL079336 Homo sapiens chromosome 20 clone RP4-662M14, ***SEQUENCING IN PROGRESS Homo sapiens 35,962 4-Feb-00 ***, 10 unorderedpieces.

1. An isolated nucleic acid molecule from Corynebacterium glutamicumencoding a stress, resistance, or tolerance gene, or a portion thereof,provided that the nucleic acid molecule does not consist of any of theF-designated genes set forth in Table
 1. 2. The isolated nucleic acidmolecule of claim 1, wherein said stress, resistance, or tolerance geneis selected from the group consisting of nucleic acid molecules involvedin a stress response, tolerance, or resistance to temperature stresses,pH stresses, oxygen stresses, osmotic stresses, toxic chemicals, oxygenradicals, antibiotics, or to lincomycin.
 3. An isolated Corynebacteriumglutamicum nucleic acid molecule selected from the group consisting ofthose sequences set forth in Appendix A, or a portion thereof, providedthat the nucleic acid molecule does not consist of any of theF-designated genes set forth in Table
 1. 4. An isolated nucleic acidmolecule which encodes a polypeptide sequence selected from the groupconsisting of those sequences set forth in Appendix B, provided that thenucleic acid molecule does not consist of any of the F-designated genesset forth in Table
 1. 5. An isolated nucleic acid molecule which encodesa naturally occurring allelic variant of a polypeptide selected from thegroup of amino acid sequences consisting of those sequences set forth inAppendix B, provided that the nucleic acid molecule does not consist ofany of the F-designated genes set forth in Table
 1. 6. An isolatednucleic acid molecule comprising a nucleotide sequence which is at least50% homologous to a nucleotide sequence selected from the groupconsisting of those sequences set forth in Appendix A, or a portionthereof, provided that the nucleic acid molecule does not consist of anyof the F-designated genes set forth in Table
 1. 7. An isolated nucleicacid molecule comprising a fragment of at least 15 nucleotides of anucleic acid comprising a nucleotide sequence selected from the groupconsisting of those sequences set forth in Appendix A, provided that thenucleic acid molecule does not consist of any of the F-designated genesset forth in Table
 1. 8. An isolated nucleic acid molecule whichhybridizes to the nucleic acid molecule of any one of claims 1-7 understringent conditions.
 9. An isolated nucleic acid molecule comprisingthe nucleic acid molecule of claim 1 or a portion thereof and anucleotide sequence encoding a heterologous polypeptide.
 10. A vectorcomprising the nucleic acid molecule of claim
 1. 11. The vector of claim10, which is an expression vector.
 12. A host cell transfected with theexpression vector of claim
 11. 13. The host cell of claim 12, whereinsaid cell is a microorganism.
 14. The host cell of claim 13, whereinsaid cell belongs to the genus Corynebacterium or Brevibacterium. 15.The host cell of claim. 12, wherein the expression of said nucleic acidmolecule results in the modulation in production of a fine chemical fromsaid cell.
 16. The host cell of claim 15, wherein said fine chemical isselected from the group consisting of: organic acids, proteinogenic andnonproteinogenic amino acids, purine and pyrimidine bases, nucleosides,nucleotides, lipids, saturated and unsaturated fatty acids, diols,carbohydrates, aromatic compounds, vitamins, cofactors, polyketides, andenzymes.
 17. A method of producing a polypeptide comprising culturingthe host cell of claim 12 in an appropriate culture medium to, thereby,produce the polypeptide.
 18. An isolated stress, resistance, ortolerance polypeptide from Corynebacterium glutamicum, or a portionthereof.
 19. The protein of claim 18, wherein said stress, resistance,or tolerance polypeptide is selected from the group consisting ofproteins involved in a stress response, tolerance, or resistance totemperature stresses, pH stresses, oxygen stresses, osmotic stresses,toxic chemicals, oxygen radicals, antibiotics, or to lincomycin.
 20. Anisolated polypeptide comprising an amino acid sequence selected from thegroup consisting of those sequences set forth in Appendix B, providedthat the amino acid sequence is not encoded by any of the F-designatedgenes set forth in Table
 1. 21. An isolated polypeptide comprising anaturally occurring allelic variant of a polypeptide comprising an aminoacid sequence selected from the group consisting of those sequences setforth in Appendix B, or a portion thereof, provided that the amino acidsequence is not encoded by any of the F-designated genes set forth inTable
 1. 22. The isolated polypeptide of claim 18, further comprisingheterologous amino acid sequences.
 23. An isolated polypeptide which isencoded by a nucleic acid molecule comprising a nucleotide sequencewhich is at least 50% homologous to a nucleic acid selected from thegroup consisting of those sequences set forth in Appendix A, providedthat the nucleic acid molecule does not consist of any of theF-designated nucleic acid molecules set forth in Table
 1. 24. Anisolated polypeptide comprising an amino acid sequence which is at least50% homologous to an amino acid sequence selected from the groupconsisting of those sequences set forth in Appendix B, provided that theamino acid sequence is not encoded by any of the F-designated genes setforth in Table
 1. 25. A method for producing a fine chemical, comprisingculturing a cell containing a vector of claim 12 such that the finechemical is produced.
 26. The method of claim 25, wherein said methodfurther comprises the step of recovering the fine chemical from saidculture.
 27. The method of claim 25, wherein said method furthercomprises the step of transfecting said cell with the vector of claim 11to result in a cell containing said vector.
 28. The method of claim 25,wherein said cell belongs to the genus Corynebacterium orBrevibacterium.
 29. The method of claim 25, wherein said cell isselected from the group consisting of: Corynebacterium glutamicum,Corynebacterium herculis, Corynebacterium, lilium, Corynebacteriumacetoacidophilum, Corynebacterium acetoglutamicum, Corynebacteriumacetophilum, Corynebacterium ammoniagenes, Corynebacterium fujiokense,Corynebacterium nitrilophilus, Brevibacterium ammoniagenes,Brevibacterium butanicum, Brevibacterium divaricatum, Brevibacteriumflavum, Brevibacterium healii, Brevibacterium ketoglutamicum,Brevibacterium ketosoreduclum, Brevibacterium lactofermentum,Brevibacterium linens, Brevibacterium paraffinolyticum, and thosestrains set forth in Table
 3. 30. The method of claim 25, whereinexpression of the nucleic acid molecule from said vector results inmodulation of production of said fine chemical.
 31. The method of claim25, wherein said fine chemical is selected from the group consisting of:organic acids, proteinogenic and nonproteinogenic amino acids, purineand pyrimidine bases, nucleosides, nucleotides, lipids, saturated andunsaturated fatty acids, diols, carbohydrates, aromatic compounds,vitamins, cofactors, polyketides and enzymes.
 32. The method of claim25, wherein said fine chemical is an amino acid.
 33. The method of claim32, wherein said amino acid is drawn from the group consisting of:lysine, glutamate, glutamine, alanine, aspartate, glycine, serine,threonine, methionine, cysteine, valine, leucine, isoleucine, arginine,proline, histidine, tyrosine, phenylalanine, and tryptophan.
 34. Amethod for producing a fine chemical, comprising culturing a cell whosegenomic DNA has been altered by the inclusion of a nucleic acid moleculeof any one of claims 1-9.
 35. A method for diagnosing the presence oractivity of Corynebacterium diphtheriae in a subject, comprisingdetecting the presence of one or more of the sequences set forth inAppendix A or Appendix B in the subject, provided that the sequences arenot or are not encoded by any of the F-designated sequences set forth inTable 1, thereby diagnosing the presence or activity of Corynebacteriumdiphtheriae in the subject.
 36. A host cell comprising a nucleic acidmolecule selected from the group consisting of the nucleic acidmolecules set forth in Appendix A, wherein the nucleic acid molecule isdisrupted.
 37. A host cell comprising a nucleic acid molecule selectedfrom the group consisting of the nucleic acid molecules set forth inAppendix A, wherein the nucleic acid molecule comprises one or morenucleic acid modifications from the sequence set forth in Appendix A.38. A host cell comprising a nucleic acid molecule selected from thegroup consisting of the nucleic acid molecules set forth in Appendix A,wherein the regulatory region of the nucleic acid molecule is modifiedrelative to the wild-type regulatory region of the molecule.